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/7769638/working'
mkdir: created directory `/scratch/stefan/7769638/working/protonate'
Storing results in /scratch/stefan/7769638/finished
Working in /scratch/stefan/7769638/working
/scratch/stefan/7769638/working /scratch/stefan/7769638

/scratch/stefan/7769638/working/protonate /scratch/stefan/7769638/working /scratch/stefan/7769638
Precomputing protomers for all compounds (pH: 7.4)
awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory)
chmod: cannot access `/nfs/home/stefan/.install4j': No such file or directory
Nov 27, 2019 6:16:53 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:23 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:24 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 6:17:41 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:41 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:41 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:41 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:41 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:53 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:53 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:54 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 6:18:01 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:01 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:01 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:01 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:01 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:15 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:23 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:24 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 6:18:29 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:29 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:29 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:29 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:29 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:43 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:43 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:43 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:43 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:43 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
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 6:18:58 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:58 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:58 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:58 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:58 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:23 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:23 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:23 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:31 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 6:19:46 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:47 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:47 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:47 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:47 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:47 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:53 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:53 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:04 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:04 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:04 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:04 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:04 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:23 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:23 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:23 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:23 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:33 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:33 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:33 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:33 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:33 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:33 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:33 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:33 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:34 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:34 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:34 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:34 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:34 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
ph 7.4: 1071 protomers created
Coalesing and merging protomers
1028 protomers generated for 1000 compounds
Checking for new stereocenters and expanding
1039 protomers after new stereo-center expansion
/scratch/stefan/7769638/working /scratch/stefan/7769638

Bulk generating 3D conformations all protomers in /scratch/stefan/7769638/working/3D
mkdir: created directory `/scratch/stefan/7769638/working/3D'
We are using corina for 3D embeding
debuging info:: /scratch/stefan/7769638/working/protonate/xaaaacf-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'
1040 3D conformations generated for 1000 compounds

Building REAL300000057001
mkdir: created directory `/scratch/stefan/7769638/working/building'
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057001'
/scratch/stefan/7769638/working/building/REAL300000057001 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057001

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057001/0 /scratch/stefan/7769638/working/building/REAL300000057001 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1
`/scratch/stefan/7769638/working/3D/1' -> `0.mol2'
Preparing input files

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

`REAL300000057001.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057001.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057001/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057001 none CCSCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 168, 98, 25, 25, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 48, 48, 40, 48, 48, 201, 201, 201, 201, 201, 98, 98, 11, 7, 1, 1, 1, 1, 48, 48, 40, 48, 48] 201
rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42])
total number of confs: 707
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057001 none CCSCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 50, 22, 4, 1, 4, 4, 13, 13, 13, 33, 48, 48, 39, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 22, 22, 13, 33, 48, 48, 48, 48, 1, 1, 1, 1, 1] 201
rigid atoms, others: [4, 38, 39, 40, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 367
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057001 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057001
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `/scratch/stefan/7769638/finished'
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057001/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057001
Building REAL300000057002
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057002'
/scratch/stefan/7769638/working/building/REAL300000057002 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057002

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057002/0 /scratch/stefan/7769638/working/building/REAL300000057002 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 2)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/2
`/scratch/stefan/7769638/working/3D/2' -> `0.mol2'
Preparing input files

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

`REAL300000057002.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057002.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057002/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057002 none CC(CCCCNC(=O)OC(C)(C)C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 51, 59, 84, 152, 200, 200, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 43, 43, 59, 59, 59, 59, 84, 84, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [19, 25, 54, 18, 51, 20, 21, 22, 23, 24, 52, 26, 27, 53] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 820
number of broken/clashed sets: 200
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057002 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057002
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057002/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057002
Building REAL300000057003
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057003'
/scratch/stefan/7769638/working/building/REAL300000057003 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057003

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057003/0 /scratch/stefan/7769638/working/building/REAL300000057003 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 3)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/3
`/scratch/stefan/7769638/working/3D/3' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCC2=C1F)

`REAL300000057003.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057003.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057003/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057003 none COC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCC2=C1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 15, 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, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 29, 29, 27, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 7, 25, 29, 29, 29, 29, 1, 1, 1, 1] 29
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 21, 22, 23, 24, 25, 38, 29, 30, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 85
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057003 none COC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCC2=C1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 15, 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, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 7, 1, 1, 1, 1, 29, 29, 29, 29] 29
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 71
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057003 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057003
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057003/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057003
Building REAL300000057004
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057004'
/scratch/stefan/7769638/working/building/REAL300000057004 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057004

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057004/0 /scratch/stefan/7769638/working/building/REAL300000057004 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 4)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/4
`/scratch/stefan/7769638/working/3D/4' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)=CC1=CC=CC=C1OC(F)F)

`REAL300000057004.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057004.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057004/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057004 none CC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)=CC1=CC=CC=C1OC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 51, 51, 108, 108, 91, 108, 108, 108, 201, 201, 201, 51, 51, 51, 16, 6, 6, 1, 1, 1, 1, 51, 108, 108, 108, 108, 201] 201
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43])
total number of confs: 455
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057004 none CC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)=CC1=CC=CC=C1OC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 26, 42, 42, 42, 92, 108, 108, 103, 104, 108, 108, 108, 108, 1, 1, 1, 1, 1, 1, 1, 1, 9, 40, 40, 5, 5, 5, 26, 42, 92, 108, 108, 108, 108, 5, 1, 1, 1, 1, 40] 201
rigid atoms, others: [39, 40, 41, 42, 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, 43])
total number of confs: 467
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057004 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057004
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057004/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057004
Building REAL300000057005
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057005'
/scratch/stefan/7769638/working/building/REAL300000057005 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057005

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057005/0 /scratch/stefan/7769638/working/building/REAL300000057005 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 5)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/5
`/scratch/stefan/7769638/working/3D/5' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Cl)=CC(Cl)=C2[N+](=O)[O-])C=C1)

`REAL300000057005.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057005/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057005 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Cl)=CC(Cl)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.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, 11, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 11, 11, 1, 1, 7, 7, 6, 6, 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, 7, 7, 3, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 34, 34, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 8, 14, 34, 49, 49, 1, 1] 49
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32])
total number of confs: 96
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057005 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Cl)=CC(Cl)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.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, 11, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 11, 11, 1, 1, 7, 7, 6, 6, 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, 7, 7, 3, 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, 21, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 55, 55, 55, 55, 55, 21, 7, 1, 1, 55, 55] 55
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 147
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057005 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057005
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057005/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057005
Building REAL300000057006
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057006'
/scratch/stefan/7769638/working/building/REAL300000057006 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057006

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057006/0 /scratch/stefan/7769638/working/building/REAL300000057006 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 6)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/6
`/scratch/stefan/7769638/working/3D/6' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC3=CC(C(=O)[O-])=CC=C32)C=C1)

`REAL300000057006.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057006.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057006/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057006 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC3=CC(C(=O)[O-])=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 6, 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, 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, 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, 7, 14, 14, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 7, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057006 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC3=CC(C(=O)[O-])=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 6, 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, 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, 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, 7, 6, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 43, 44, 26, 27, 28, 29, 30, 31])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057006 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057006
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057006/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057006
Building REAL300000057007
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057007'
/scratch/stefan/7769638/working/building/REAL300000057007 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057007

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057007/0 /scratch/stefan/7769638/working/building/REAL300000057007 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 7)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/7
`/scratch/stefan/7769638/working/3D/7' -> `0.mol2'
Preparing input files

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

`REAL300000057007.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057007.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057007/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057007 none CN(C)C1=NC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 5, 5, 16, 16, 16, 37, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 3, 3, 1, 1, 1, 5, 16, 37, 38, 38, 38, 38] 38
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057007 none CN(C)C1=NC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 26, 26, 15, 15, 6, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 15, 6, 1, 1, 1, 1] 38
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057007 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057007/1 /scratch/stefan/7769638/working/building/REAL300000057007 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 8)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/8
`/scratch/stefan/7769638/working/3D/8' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=[NH+]C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057007.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057007.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057007/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057007 none CN(C)C1=[NH+]C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 8, 6, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 16, 28, 28, 28, 28, 28] 28
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 33, 31] set([0, 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])
total number of confs: 85
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057007 none CN(C)C1=[NH+]C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 8, 6, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 19, 19, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 8, 6, 1, 1, 1, 1] 28
rigid atoms, others: [37, 38, 39, 40, 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, 36])
total number of confs: 56
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057007 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057007
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057007/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057007/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057007
Building REAL300000057008
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057008'
/scratch/stefan/7769638/working/building/REAL300000057008 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057008

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057008/0 /scratch/stefan/7769638/working/building/REAL300000057008 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 9)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/9
`/scratch/stefan/7769638/working/3D/9' -> `0.mol2'
Preparing input files

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

`REAL300000057008.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057008.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057008/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057008 none NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['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.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']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 3, 1, 1, 1, 1, 1, 6, 6, 23, 24, 24, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 3, 3, 1, 1, 6, 23, 41, 41, 41, 41, 41, 1, 1] 62
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 126
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057008 none NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['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.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']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 39, 62, 62, 23, 41, 41, 23, 23, 8, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 62, 62, 41, 41, 23, 8, 7, 1, 1, 1, 1, 41, 41] 62
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: 286
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057008 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057008
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057008/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057008
Building REAL300000057009
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057009'
/scratch/stefan/7769638/working/building/REAL300000057009 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057009

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057009/0 /scratch/stefan/7769638/working/building/REAL300000057009 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 10)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/10
`/scratch/stefan/7769638/working/3D/10' -> `0.mol2'
Preparing input files

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

`REAL300000057009.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057009.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057009/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057009 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(C)NC(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 32, 32, 71, 94, 94, 110, 110, 110, 110, 14, 14, 14, 8, 6, 1, 1, 1, 1, 32, 32, 32, 32, 71, 110, 110, 110, 110, 110, 110, 110, 110, 110] 110
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 349
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057009 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057009
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057009/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057009
Building REAL300000057010
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057010'
/scratch/stefan/7769638/working/building/REAL300000057010 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057010

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057010/0 /scratch/stefan/7769638/working/building/REAL300000057010 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 11)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/11
`/scratch/stefan/7769638/working/3D/11' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1CCC(=O)N1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057010.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057010.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057010/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057010 none CC(CC1CCC(=O)N1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 5, 5, 5, 5, 1, 11, 8, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 6, 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]
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: [43, 8, 1, 1, 1, 1, 1, 1, 1, 43, 43, 111, 111, 111, 165, 166, 166, 165, 166, 166, 166, 166, 166, 43, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 111, 165, 166, 166, 166, 166] 166
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39])
total number of confs: 494
number of broken/clashed sets: 103
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057010 none CC(CC1CCC(=O)N1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 5, 5, 5, 5, 1, 11, 8, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 6, 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]
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: [48, 48, 48, 145, 166, 166, 166, 166, 166, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 145, 145, 166, 166, 166, 166, 166, 166, 16, 7, 1, 1, 1, 1] 166
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 554
number of broken/clashed sets: 103
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057010 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057010
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057010/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057010
Building REAL300000057011
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057011'
/scratch/stefan/7769638/working/building/REAL300000057011 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057011

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057011/0 /scratch/stefan/7769638/working/building/REAL300000057011 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 12)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/12
`/scratch/stefan/7769638/working/3D/12' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1N1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1)

`REAL300000057011.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057011.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057011/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057011 none CC1=CC=CC=C1N1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 38, 38, 38, 66, 70, 70, 66, 70, 70, 70, 70, 70, 8, 8, 2, 2, 2, 1, 1, 1, 1, 8, 18, 38, 66, 70, 70, 70, 70] 70
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057011 none CC1=CC=CC=C1N1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [8, 8, 8, 1, 8, 8, 1, 1, 1, 1, 1, 7, 7, 19, 20, 20, 50, 54, 54, 50, 52, 54, 54, 54, 54, 1, 1, 8, 8, 8, 8, 1, 8, 8, 1, 7, 19, 50, 54, 54, 54, 54] 70
rigid atoms, others: [34, 6, 7, 8, 9, 10, 25, 26] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057011 none CC1=CC=CC=C1N1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 54, 70, 70, 54, 54, 54, 39, 39, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 70, 70, 70, 70, 54, 70, 70, 54, 39, 14, 7, 1, 1, 1, 1] 70
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 146
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057011 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057011
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057011/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057011
Building REAL300000057012
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057012'
/scratch/stefan/7769638/working/building/REAL300000057012 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057012

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057012/0 /scratch/stefan/7769638/working/building/REAL300000057012 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 13)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/13
`/scratch/stefan/7769638/working/3D/13' -> `0.mol2'
Preparing input files

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

`REAL300000057012.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057012.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057012/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057012 none COC(=O)C1=CC=C([N+](=O)[O-])C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 6, 4, 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
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 22, 22, 22, 61, 72, 72, 68, 71, 72, 72, 72, 72, 1, 13, 13, 13, 1, 1, 7, 22, 61, 72, 72, 72, 72, 1] 102
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 11, 12, 40, 27, 31] set([0, 1, 3, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057012 none COC(=O)C1=CC=C([N+](=O)[O-])C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 6, 4, 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
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [102, 102, 72, 102, 72, 72, 72, 72, 72, 72, 72, 39, 39, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 72, 102, 102, 102, 72, 72, 39, 15, 7, 1, 1, 1, 1, 72] 102
rigid atoms, others: [36, 37, 38, 39, 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, 40])
total number of confs: 246
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057012 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057012
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057012/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057012
Building REAL300000057013
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057013'
/scratch/stefan/7769638/working/building/REAL300000057013 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057013

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057013/0 /scratch/stefan/7769638/working/building/REAL300000057013 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 14)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/14
`/scratch/stefan/7769638/working/3D/14' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NO1)

`REAL300000057013.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057013/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057013 none CN(C)CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [22, 8, 22, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 62, 79, 79, 70, 79, 79, 79, 79, 79, 1, 1, 22, 22, 22, 22, 22, 22, 8, 8, 1, 9, 25, 62, 79, 79, 79, 79] 158
rigid atoms, others: [32, 3, 4, 5, 6, 7, 22, 23] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 309
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057013 none CN(C)CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [158, 157, 158, 79, 79, 79, 54, 54, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 79, 79, 158, 158, 158, 158, 158, 158, 157, 157, 79, 54, 18, 7, 1, 1, 1, 1] 158
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 508
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057013 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057013/1 /scratch/stefan/7769638/working/building/REAL300000057013 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 15)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/15
`/scratch/stefan/7769638/working/3D/15' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NO1)

`REAL300000057013.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057013/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057013 none C[NH+](C)CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 44, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 7, 21, 44, 49, 49, 49, 49] 75
rigid atoms, others: [33, 4, 5, 6, 7, 8, 23, 24] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 158
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057013 none C[NH+](C)CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 75, 49, 49, 49, 36, 36, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 49, 49, 75, 75, 75, 75, 75, 75, 75, 75, 49, 36, 14, 7, 1, 1, 1, 1] 75
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])
total number of confs: 234
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057013 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057013
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057013/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057013/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057013
Building REAL300000057014
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057014'
/scratch/stefan/7769638/working/building/REAL300000057014 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057014

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057014/0 /scratch/stefan/7769638/working/building/REAL300000057014 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 16)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/16
`/scratch/stefan/7769638/working/3D/16' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=NC=C2F)C=C1)

`REAL300000057014.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057014.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057014/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057014 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=NC=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 15, 8, 1, 1, 15, 1, 1, 7, 7, 6, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 11, 11, 11, 23, 23, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 8, 11, 23, 30, 30, 1, 1] 30
rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057014 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=NC=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 15, 8, 1, 1, 15, 1, 1, 7, 7, 6, 6, 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, 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: [31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 15, 9, 1, 1, 31, 31] 31
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057014 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057014
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057014/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057014
Building REAL300000057015
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057015'
/scratch/stefan/7769638/working/building/REAL300000057015 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057015

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057015/0 /scratch/stefan/7769638/working/building/REAL300000057015 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 17)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/17
`/scratch/stefan/7769638/working/3D/17' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)(F)F)N2)C=C1)

`REAL300000057015.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057015.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057015/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057015 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)(F)F)N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 6, 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, 4, 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, 8, 10, 10, 10, 25, 25, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 8, 10, 25, 30, 30, 30, 1, 1] 30
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: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057015 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)(F)F)N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 32, 32, 32, 32, 32, 17, 7, 1, 1, 1, 32, 32] 32
rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057015 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057015
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057015/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057015
Building REAL300000057016
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057016'
/scratch/stefan/7769638/working/building/REAL300000057016 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057016

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057016/0 /scratch/stefan/7769638/working/building/REAL300000057016 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 18)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/18
`/scratch/stefan/7769638/working/3D/18' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC(C(F)(F)F)=C2)C=C1)

`REAL300000057016.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057016.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057016/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057016 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.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, 11, 8, 8, 1, 1, 1, 8, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 8, 13, 13, 13, 30, 30, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 8, 13, 30, 51, 51, 51, 1, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057016 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.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, 11, 8, 8, 1, 1, 1, 8, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 21, 20, 21, 6, 6, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 51, 51, 51, 51, 51, 20, 6, 1, 1, 1, 51, 51] 51
rigid atoms, others: [12, 13, 14, 15, 16, 17, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 143
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057016 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057016
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057016/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057016
Building REAL300000057017
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057017'
/scratch/stefan/7769638/working/building/REAL300000057017 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057017

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057017/0 /scratch/stefan/7769638/working/building/REAL300000057017 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 19)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/19
`/scratch/stefan/7769638/working/3D/19' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl)

`REAL300000057017.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057017/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057017 none NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 6, 6, 26, 27, 27, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 4, 4, 1, 1, 6, 26, 38, 38, 38, 38, 38, 1] 46
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 24, 25, 28, 29, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057017 none NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 38, 46, 46, 38, 38, 38, 19, 19, 9, 9, 7, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 46, 46, 38, 38, 19, 9, 7, 1, 1, 1, 1, 38] 46
rigid atoms, others: [33, 34, 35, 36, 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, 37])
total number of confs: 110
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057017 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057017
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057017/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057017
Building REAL300000057018
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057018'
/scratch/stefan/7769638/working/building/REAL300000057018 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057018

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057018/0 /scratch/stefan/7769638/working/building/REAL300000057018 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 20)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/20
`/scratch/stefan/7769638/working/3D/20' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCN1C=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057018.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057018/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057018 none C#CCN1C=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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: [1, 1, 5, 8, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 34, 40, 40, 34, 34, 40, 40, 40, 40, 8, 8, 8, 1, 1, 6, 14, 34, 40, 40, 40, 40] 64
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 26, 27] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057018 none C#CCN1C=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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: [1, 1, 5, 8, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 40, 40, 40, 40, 40, 28, 28, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 64, 64, 64, 40, 40, 28, 14, 7, 1, 1, 1, 1] 64
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 204
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057018 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057018
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057018/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057018
Building REAL300000057019
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057019'
/scratch/stefan/7769638/working/building/REAL300000057019 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057019

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057019/0 /scratch/stefan/7769638/working/building/REAL300000057019 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 21)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/21
`/scratch/stefan/7769638/working/3D/21' -> `0.mol2'
Preparing input files

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

`REAL300000057019.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057019.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057019/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057019 none CCOC(=O)CC(C)(C)C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [119, 113, 113, 51, 113, 32, 12, 32, 32, 12, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 51, 51, 32, 32, 32, 32, 32, 32, 12, 6, 6, 1, 1, 1, 1] 119
rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 423
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057019 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057019
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057019/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057019
Building REAL300000057020
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057020'
/scratch/stefan/7769638/working/building/REAL300000057020 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057020

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057020/0 /scratch/stefan/7769638/working/building/REAL300000057020 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 22)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/22
`/scratch/stefan/7769638/working/3D/22' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2[C@@H]3CCC[C@H]2CC2=CC=CC=C2C3)C=C1)

`REAL300000057020.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057020/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057020 none O=C([O-])C1=CC=C(NC(=O)NN=C2[C@@H]3CCC[C@H]2CC2=CC=CC=C2C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 8, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1] 28
rigid atoms, others: [1, 3, 4, 5, 6, 7, 48, 49, 28, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 56
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057020 none O=C([O-])C1=CC=C(NC(=O)NN=C2[C@@H]3CCC[C@H]2CC2=CC=CC=C2C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 28
rigid atoms, others: [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, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 48, 49, 32, 33, 28, 29, 30, 31])
total number of confs: 71
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057020 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057020
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057020/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057020
Building REAL300000057021
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057021'
/scratch/stefan/7769638/working/building/REAL300000057021 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057021

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057021/0 /scratch/stefan/7769638/working/building/REAL300000057021 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 23)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/23
`/scratch/stefan/7769638/working/3D/23' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1O)

`REAL300000057021.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057021/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057021 none COC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7]
1  hydrogens need rotated
278  conformations in input
total number of sets (complete confs): 278
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 62, 63, 63, 135, 139, 139, 139, 139, 139, 139, 139, 139, 1, 1, 1, 4, 4, 4, 1, 1, 13, 13, 13, 62, 135, 139, 139, 139, 139, 1, 2] 278
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 22, 23, 24, 28, 29] set([0, 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, 40])
total number of confs: 394
number of broken/clashed sets: 178
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057021 none COC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7]
1  hydrogens need rotated
278  conformations in input
total number of sets (complete confs): 278
using faster count positions algorithm for large data
unique positions, atoms: [139, 139, 139, 139, 139, 49, 49, 49, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 139, 139, 139, 139, 49, 49, 49, 14, 7, 1, 1, 1, 1, 139, 278] 278
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40])
total number of confs: 485
number of broken/clashed sets: 178
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057021 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057021
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057021/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057021
Building REAL300000057022
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057022'
/scratch/stefan/7769638/working/building/REAL300000057022 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057022

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057022/0 /scratch/stefan/7769638/working/building/REAL300000057022 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 24)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/24
`/scratch/stefan/7769638/working/3D/24' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC=CC2=CC=CC=C21)

`REAL300000057022.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057022.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057022/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057022 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC=CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 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: [7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 53, 53, 53, 53, 53, 53, 53, 53, 53, 36, 36, 36, 15, 7, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53] 53
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 102
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057022 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC=CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 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: [7, 7, 7, 4, 7, 6, 4, 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]
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: [10, 1, 10, 10, 29, 29, 29, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1] 53
rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 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])
total number of confs: 141
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057022 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057022
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057022/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057022
Building REAL300000057023
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057023'
/scratch/stefan/7769638/working/building/REAL300000057023 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057023

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057023/0 /scratch/stefan/7769638/working/building/REAL300000057023 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 25)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/25
`/scratch/stefan/7769638/working/3D/25' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CCCC3)CC2)C=C1)

`REAL300000057023.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057023/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057023 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CCCC3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 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, 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, 8, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 8, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 32
rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 71
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057023 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CCCC3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 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, 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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 32
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 44, 45, 22, 23, 24, 25, 26, 27])
total number of confs: 79
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057023 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057023
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057023/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057023
Building REAL300000057024
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057024'
/scratch/stefan/7769638/working/building/REAL300000057024 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057024

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057024/0 /scratch/stefan/7769638/working/building/REAL300000057024 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 26)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/26
`/scratch/stefan/7769638/working/3D/26' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057024.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057024/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057024 none CC(C)(C)C1CCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 18] 20
rigid atoms, others: [32, 1, 34, 35, 4, 5, 6, 7, 8, 9, 33, 31] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 56
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057024 none CC(C)(C)C1CCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 18, 20, 20, 18, 18, 18, 18, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 18, 18, 18, 18, 18, 12, 7, 1, 1, 1, 1] 20
rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 61
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057024 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057024
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057024/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057024
Building REAL300000057025
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057025'
/scratch/stefan/7769638/working/building/REAL300000057025 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057025

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057025/0 /scratch/stefan/7769638/working/building/REAL300000057025 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 27)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/27
`/scratch/stefan/7769638/working/3D/27' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C(F)F)C2)C=C1)

`REAL300000057025.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057025/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057025 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C(F)F)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 15, 15, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 55, 55, 55, 55, 55, 55, 56, 56, 55, 1, 1, 1, 1, 10, 16, 55, 55, 55, 55, 55, 55, 55, 56, 55, 55, 1, 1] 56
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 100
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057025 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C(F)F)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 15, 15, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 51, 55, 51, 55, 55, 44, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 55, 55, 55, 55, 44, 9, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 55, 55] 56
rigid atoms, others: [32, 33, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 18, 19, 21, 22, 23, 24, 25, 26, 38, 37])
total number of confs: 167
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057025 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057025
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057025/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057025
Building REAL300000057026
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057026'
/scratch/stefan/7769638/working/building/REAL300000057026 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057026

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057026/0 /scratch/stefan/7769638/working/building/REAL300000057026 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 28)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/28
`/scratch/stefan/7769638/working/3D/28' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=CC=C2NC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1)

`REAL300000057026.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057026.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057026/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057026 none CC(C)(C)C1=CC=C2NC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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.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, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33, 33, 114, 144, 144, 128, 128, 144, 144, 144, 144, 1, 1, 3, 3, 3, 2, 2, 2, 3, 3, 3, 1, 1, 1, 1, 10, 32, 114, 144, 144, 144, 144, 1] 144
rigid atoms, others: [1, 11, 4, 5, 6, 7, 38, 9, 10, 39, 48, 8, 40, 26, 27, 37] set([0, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 474
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057026 none CC(C)(C)C1=CC=C2NC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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.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, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 60, 60, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 140, 144, 144, 60, 18, 7, 1, 1, 1, 1, 144] 144
rigid atoms, others: [44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48])
total number of confs: 236
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057026 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057026
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057026/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057026
Building REAL300000057027
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057027'
/scratch/stefan/7769638/working/building/REAL300000057027 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057027

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057027/0 /scratch/stefan/7769638/working/building/REAL300000057027 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 29)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/29
`/scratch/stefan/7769638/working/3D/29' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Br)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057027.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057027.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057027/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057027 none CC1=CC(Br)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 13, 13, 29, 29, 29, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 2, 2, 2, 1, 13, 29, 52, 52, 52, 52, 52] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057027 none CC1=CC(Br)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 34, 34, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 34, 13, 7, 1, 1, 1, 1] 52
rigid atoms, others: [32, 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: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057027 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057027
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057027/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057027
Building REAL300000057028
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057028'
/scratch/stefan/7769638/working/building/REAL300000057028 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057028

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057028/0 /scratch/stefan/7769638/working/building/REAL300000057028 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 30)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/30
`/scratch/stefan/7769638/working/3D/30' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)N1CCOCC1)

`REAL300000057028.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057028.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057028/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057028 none CC(C)(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)N1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [88, 36, 88, 36, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 132, 132, 132, 132, 132, 88, 88, 88, 88, 88, 88, 36, 16, 7, 1, 1, 1, 1, 132, 132, 132, 132, 132, 132, 132, 132] 132
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 370
number of broken/clashed sets: 91
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057028 none CC(C)(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)N1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 40, 40, 69, 70, 70, 132, 132, 132, 132, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 1, 10, 10, 10, 9, 9, 9, 40, 69, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 1, 1, 1] 132
rigid atoms, others: [1, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 392
number of broken/clashed sets: 91
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057028 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057028
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057028/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057028
Building REAL300000057029
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057029'
/scratch/stefan/7769638/working/building/REAL300000057029 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057029

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057029/0 /scratch/stefan/7769638/working/building/REAL300000057029 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 31)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/31
`/scratch/stefan/7769638/working/3D/31' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057029.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057029/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057029 none N#CC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 8, 16, 29, 29, 29, 29, 29] 29
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057029 none N#CC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 24, 24, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 29, 29, 29, 24, 12, 7, 1, 1, 1, 1] 29
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 60
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057029 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057029
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057029/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057029
Building REAL300000057030
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057030'
/scratch/stefan/7769638/working/building/REAL300000057030 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057030

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057030/0 /scratch/stefan/7769638/working/building/REAL300000057030 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 32)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/32
`/scratch/stefan/7769638/working/3D/32' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=CC(Cl)=C3)C2)C=C1)

`REAL300000057030.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057030/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057030 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=CC(Cl)=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 29, 29, 29, 29, 29, 29, 73, 73, 73, 73, 73, 73, 29, 1, 1, 1, 1, 8, 13, 29, 29, 29, 29, 29, 29, 29, 73, 73, 73, 73, 29, 29, 1, 1] 73
rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 129
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057030 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=CC(Cl)=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 29, 29, 29, 27, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 8, 1, 29, 29, 29, 29, 27, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 8, 9, 1, 1, 29, 29] 73
rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 43, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 44, 45])
total number of confs: 89
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057030 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=CC(Cl)=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 73, 73, 73, 72, 38, 38, 38, 9, 9, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 73, 73, 73, 73, 72, 38, 8, 9, 8, 9, 9, 9, 8, 1, 1, 1, 1, 9, 8, 73, 73] 73
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, 43, 44, 45])
total number of confs: 203
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057030 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057030
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057030/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057030
Building REAL300000057031
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057031'
/scratch/stefan/7769638/working/building/REAL300000057031 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057031

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057031/0 /scratch/stefan/7769638/working/building/REAL300000057031 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 33)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/33
`/scratch/stefan/7769638/working/3D/33' -> `0.mol2'
Preparing input files

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

`REAL300000057031.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057031/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057031 none CC(=O)NC(C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', '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, 11, 8, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [146, 146, 146, 116, 38, 38, 38, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 116, 180, 182, 159, 182, 182, 182, 146, 146, 146, 146, 116, 38, 38, 38, 14, 7, 1, 1, 1, 1, 182, 182, 182, 182] 186
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 740
number of broken/clashed sets: 147
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057031 none CC(=O)NC(C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', '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, 11, 8, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 10, 1, 10, 32, 32, 32, 92, 92, 92, 172, 182, 182, 172, 174, 182, 182, 182, 182, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 10, 32, 32, 32, 92, 172, 182, 182, 182, 182, 1, 1, 1, 1] 186
rigid atoms, others: [4, 42, 43, 44, 45, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 606
number of broken/clashed sets: 147
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057031 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057031
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057031/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057031
Building REAL300000057032
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057032'
/scratch/stefan/7769638/working/building/REAL300000057032 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057032

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057032/0 /scratch/stefan/7769638/working/building/REAL300000057032 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 34)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/34
`/scratch/stefan/7769638/working/3D/34' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@H+](C3CC3)C(C3=CC=CC=C3)C2)C=C1)

`REAL300000057032.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057032.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057032/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057032 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@H+](C3CC3)C(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 6, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 51, 52, 28, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 42
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057032 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@H+](C3CC3)C(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 21, 21, 21, 21, 19, 11, 3, 3, 3, 3, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 3, 3, 21, 21] 21
rigid atoms, others: [44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51, 52])
total number of confs: 61
number of broken/clashed sets: 21
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057032 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@H+](C3CC3)C(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 3, 3, 1, 3, 3, 1, 21, 21, 21, 21, 18, 8, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 3, 3, 1, 3, 3, 1, 1, 21, 21] 21
rigid atoms, others: [34, 35, 36, 37, 49, 10, 11, 12, 13, 14, 15, 16, 17, 50, 20, 21, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 51, 52])
total number of confs: 70
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057032 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@H+](C3CC3)C(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 13, 13, 13, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 19, 13, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21] 21
rigid atoms, others: [38, 39, 40, 41, 42, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 55
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057032 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057032/1 /scratch/stefan/7769638/working/building/REAL300000057032 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 35)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/35
`/scratch/stefan/7769638/working/3D/35' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@@H+](C3CC3)C(C3=CC=CC=C3)C2)C=C1)

`REAL300000057032.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057032.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057032/1/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', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057032 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@@H+](C3CC3)C(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 7, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16
rigid atoms, others: [1, 3, 4, 5, 6, 7, 51, 52, 28, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 38
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057032 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@@H+](C3CC3)C(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 16, 16, 15, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 15, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 16, 16] 16
rigid atoms, others: [44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51, 52])
total number of confs: 48
number of broken/clashed sets: 16
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057032 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@@H+](C3CC3)C(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 16, 16, 15, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 2, 2, 1, 16, 16, 16, 16, 15, 7, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 1, 1, 16, 16] 16
rigid atoms, others: [34, 35, 36, 37, 49, 10, 11, 12, 13, 14, 15, 16, 17, 50, 20, 21, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 51, 52])
total number of confs: 55
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057032 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@@H+](C3CC3)C(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 16, 16, 15, 7, 7, 7, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 15, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16] 16
rigid atoms, others: [38, 39, 40, 41, 42, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 48
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057032 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057032
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057032/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057032/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057032
Building REAL300000057033
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057033'
/scratch/stefan/7769638/working/building/REAL300000057033 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057033

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057033/0 /scratch/stefan/7769638/working/building/REAL300000057033 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 36)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/36
`/scratch/stefan/7769638/working/3D/36' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=NC=NN21)

`REAL300000057033.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057033/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057033 none CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=NC=NN21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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
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, 5, 6, 6, 19, 20, 20, 19, 19, 20, 20, 20, 20, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 5, 19, 20, 20, 20, 20, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 18, 19, 20, 21, 22, 26, 27, 28] set([32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 29, 30, 31])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057033 none CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=NC=NN21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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
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, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 18, 7, 1, 1, 1, 1, 20] 20
rigid atoms, others: [32, 33, 34, 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, 35])
total number of confs: 51
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057033 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057033
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057033/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057033
Building REAL300000057034
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057034'
/scratch/stefan/7769638/working/building/REAL300000057034 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057034

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057034/0 /scratch/stefan/7769638/working/building/REAL300000057034 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 37)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/37
`/scratch/stefan/7769638/working/3D/37' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCOC1)

`REAL300000057034.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057034/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057034 none COC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 1, 1, 12, 12, 31, 31, 31, 68, 76, 76, 68, 68, 76, 76, 76, 76, 1, 1, 1, 1, 5, 5, 5, 12, 31, 68, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1] 78
rigid atoms, others: [32, 1, 2, 3, 36, 37, 35, 33, 34, 18, 19, 20, 21] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 258
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057034 none COC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 76, 29, 29, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 76, 76, 76, 76, 78, 78, 78, 29, 14, 7, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76] 78
rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37])
total number of confs: 187
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057034 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057034
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057034/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057034
Building REAL300000057035
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057035'
/scratch/stefan/7769638/working/building/REAL300000057035 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057035

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057035/0 /scratch/stefan/7769638/working/building/REAL300000057035 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 38)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/38
`/scratch/stefan/7769638/working/3D/38' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=CC=CC2=C1NC(=O)C2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057035.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057035.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057035/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057035 none CC(C)C1=CC=CC2=C1NC(=O)C2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 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]
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, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 19, 20, 20, 19, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 19, 20, 20, 20, 20] 20
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 36, 37] set([0, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057035 none CC(C)C1=CC=CC2=C1NC(=O)C2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 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]
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, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 14, 7, 1, 1, 1, 1] 20
rigid atoms, others: [40, 41, 42, 43, 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, 38, 39])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057035 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057035
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057035/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057035
Building REAL300000057036
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057036'
/scratch/stefan/7769638/working/building/REAL300000057036 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057036

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057036/0 /scratch/stefan/7769638/working/building/REAL300000057036 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 39)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/39
`/scratch/stefan/7769638/working/3D/39' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1)

`REAL300000057036.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057036.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057036/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057036 none NC(=O)CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 6, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 9, 50, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 61, 80, 80, 61, 61, 80, 80, 80, 80, 1, 1, 50, 50, 9, 9, 1, 8, 26, 61, 80, 80, 80, 80] 201
rigid atoms, others: [3, 4, 5, 6, 7, 22, 23, 28] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 448
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057036 none NC(=O)CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 6, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 201, 80, 80, 80, 46, 46, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 80, 80, 201, 201, 173, 173, 80, 46, 16, 7, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 658
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057036 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057036
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057036/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057036
Building REAL300000057037
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057037'
/scratch/stefan/7769638/working/building/REAL300000057037 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057037

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057037/0 /scratch/stefan/7769638/working/building/REAL300000057037 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 40)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/40
`/scratch/stefan/7769638/working/3D/40' -> `0.mol2'
Preparing input files

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

`REAL300000057037.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057037/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057037 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [46, 30, 30, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 41, 41, 30, 41, 41, 46, 46, 46, 46, 46, 13, 7, 1, 1, 1, 1, 41, 41, 41, 41] 48
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 204
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057037 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [17, 7, 1, 7, 7, 28, 28, 28, 40, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 28, 40, 41, 41, 41, 41, 1, 1, 1, 1] 48
rigid atoms, others: [34, 35, 36, 37, 2, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 154
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057037 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057037
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057037/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057037
Building REAL300000057038
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057038'
/scratch/stefan/7769638/working/building/REAL300000057038 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057038

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057038/0 /scratch/stefan/7769638/working/building/REAL300000057038 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 41)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/41
`/scratch/stefan/7769638/working/3D/41' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CC(CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057038.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057038.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057038/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057038 none CC(C)(C)OC(=O)N1CC(CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 6, 7, 7, 2, 1, 2, 1, 1, 1, 1, 7, 47, 47, 50, 50, 50, 90, 90, 90, 90, 90, 90, 90, 90, 90, 1, 8, 8, 8, 7, 7, 7, 8, 8, 8, 1, 1, 1, 7, 7, 47, 50, 90, 90, 90, 90, 90, 1, 1] 201
rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 48, 49, 26, 37] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 288
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057038 none CC(C)(C)OC(=O)N1CC(CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 129, 90, 129, 90, 90, 43, 9, 9, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 90, 90, 43, 43, 9, 6, 6, 1, 1, 1, 1, 90, 90] 201
rigid atoms, others: [44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49])
total number of confs: 564
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057038 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057038
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057038/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057038
Building REAL300000057039
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057039'
/scratch/stefan/7769638/working/building/REAL300000057039 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057039

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057039/0 /scratch/stefan/7769638/working/building/REAL300000057039 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 42)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/42
`/scratch/stefan/7769638/working/3D/42' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=C1)OC(C)(C)CC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057039.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057039/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057039 none COC1=CC=C2C(=C1)OC(C)(C)CC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.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', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 34, 43, 43, 40, 41, 43, 43, 43, 43, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 9, 34, 43, 43, 43, 43] 43
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 33, 31] set([0, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47])
total number of confs: 133
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057039 none COC1=CC=C2C(=C1)OC(C)(C)CC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.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', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 43, 43, 43, 43, 43, 43, 43, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 16, 7, 1, 1, 1, 1] 43
rigid atoms, others: [44, 45, 46, 47, 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, 40, 41, 42, 43])
total number of confs: 80
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057039 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057039
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057039/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057039
Building REAL300000057040
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057040'
/scratch/stefan/7769638/working/building/REAL300000057040 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057040

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057040/0 /scratch/stefan/7769638/working/building/REAL300000057040 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 43)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/43
`/scratch/stefan/7769638/working/3D/43' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1)

`REAL300000057040.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057040.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057040/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057040 none CC1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 32, 32, 32, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 2, 2, 2, 1, 12, 32, 75, 75, 75, 75, 75, 1] 75
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 21, 22, 23, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057040 none CC1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 35, 75, 75, 75, 35, 35, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 75, 75, 75, 75, 75, 75, 75, 35, 18, 7, 1, 1, 1, 1, 75] 75
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 271
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057040 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057040
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057040/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057040
Building REAL300000057041
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057041'
/scratch/stefan/7769638/working/building/REAL300000057041 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057041

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057041/0 /scratch/stefan/7769638/working/building/REAL300000057041 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 44)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/44
`/scratch/stefan/7769638/working/3D/44' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CN=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057041.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057041/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057041 none COC(=O)C1=CN=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 12, 12, 12, 27, 27, 27, 47, 49, 49, 48, 48, 49, 49, 49, 49, 1, 13, 13, 13, 1, 13, 13, 13, 26, 47, 49, 49, 49, 49] 80
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 173
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057041 none COC(=O)C1=CN=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 49, 80, 49, 49, 49, 29, 29, 29, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 49, 80, 80, 80, 49, 29, 29, 29, 10, 7, 1, 1, 1, 1] 80
rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 210
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057041 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057041
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057041/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057041
Building REAL300000057042
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057042'
/scratch/stefan/7769638/working/building/REAL300000057042 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057042

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057042/0 /scratch/stefan/7769638/working/building/REAL300000057042 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 45)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/45
`/scratch/stefan/7769638/working/3D/45' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(O)=C2Br)C=C1)

`REAL300000057042.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057042/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057042 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(O)=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 28, 28, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 8, 13, 28, 33, 33, 33, 66, 1, 1] 66
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 132
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057042 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(O)=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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: [34, 34, 34, 34, 34, 34, 34, 17, 17, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 17, 8, 1, 1, 1, 2, 34, 34] 68
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057042 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057042/1 /scratch/stefan/7769638/working/building/REAL300000057042 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 46)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/46
`/scratch/stefan/7769638/working/3D/46' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC([O-])=C2Br)C=C1)

`REAL300000057042.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057042/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057042 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC([O-])=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 8, 14, 26, 26, 26, 26, 1, 1] 26
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 58
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057042 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC([O-])=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [40, 40, 40, 40, 40, 40, 39, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 39, 16, 8, 1, 1, 1, 40, 40] 40
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 101
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057042 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057042
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057042/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057042/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057042
Building REAL300000057043
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057043'
/scratch/stefan/7769638/working/building/REAL300000057043 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057043

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057043/0 /scratch/stefan/7769638/working/building/REAL300000057043 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 47)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/47
`/scratch/stefan/7769638/working/3D/47' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C[C@@H]2C[C@H]2C2=CC=CC=C2)C=C1)

`REAL300000057043.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057043/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057043 none O=C([O-])C1=CC=C(NC(=O)NN=C[C@@H]2C[C@H]2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 11, 8, 8, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 3, 5, 5, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 63
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057043 none O=C([O-])C1=CC=C(NC(=O)NN=C[C@@H]2C[C@H]2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 11, 8, 8, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [169, 163, 169, 151, 169, 169, 151, 60, 60, 60, 13, 13, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 169, 169, 169, 169, 151, 60, 13, 1, 1, 4, 4, 1, 4, 4, 169, 169] 169
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 543
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057043 none O=C([O-])C1=CC=C(NC(=O)NN=C[C@@H]2C[C@H]2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 11, 8, 8, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [169, 169, 169, 164, 169, 169, 164, 92, 92, 92, 36, 36, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 164, 92, 36, 4, 4, 1, 1, 1, 1, 1, 169, 169] 169
rigid atoms, others: [33, 34, 35, 36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39])
total number of confs: 508
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057043 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057043
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057043/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057043
Building REAL300000057044
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057044'
/scratch/stefan/7769638/working/building/REAL300000057044 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057044

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057044/0 /scratch/stefan/7769638/working/building/REAL300000057044 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 48)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/48
`/scratch/stefan/7769638/working/3D/48' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057044.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057044/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057044 none CCN1N=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 6, 6, 15, 16, 16, 38, 42, 42, 38, 40, 42, 42, 42, 42, 1, 8, 8, 8, 8, 8, 1, 6, 15, 38, 42, 42, 42, 42] 71
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057044 none CCN1N=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 42, 42, 42, 42, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 42, 71, 71, 71, 71, 71, 42, 34, 16, 7, 1, 1, 1, 1] 71
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 262
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057044 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057044
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057044/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057044
Building REAL300000057045
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057045'
/scratch/stefan/7769638/working/building/REAL300000057045 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057045

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057045/0 /scratch/stefan/7769638/working/building/REAL300000057045 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 49)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/49
`/scratch/stefan/7769638/working/3D/49' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3CC3)C=C2)C=C1)

`REAL300000057045.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057045.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057045/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057045 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3CC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 10, 10, 10, 30, 30, 34, 34, 30, 30, 55, 55, 34, 34, 1, 1, 1, 1, 8, 10, 30, 34, 34, 55, 55, 55, 55, 55, 34, 34, 1, 1] 55
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 168
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057045 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3CC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [34, 33, 34, 33, 34, 34, 33, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 34, 34, 34, 34, 33, 17, 6, 1, 1, 6, 6, 6, 6, 6, 1, 1, 34, 34] 55
rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 106
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057045 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3CC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 26, 26, 26, 14, 14, 4, 4, 6, 6, 1, 1, 1, 1, 6, 6, 55, 55, 55, 55, 55, 26, 14, 6, 6, 1, 1, 1, 1, 1, 6, 6, 55, 55] 55
rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39])
total number of confs: 163
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057045 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057045
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057045/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057045
Building REAL300000057046
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057046'
/scratch/stefan/7769638/working/building/REAL300000057046 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057046

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057046/0 /scratch/stefan/7769638/working/building/REAL300000057046 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 50)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/50
`/scratch/stefan/7769638/working/3D/50' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CC3)N=C2)C=C1)

`REAL300000057046.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057046.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057046/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057046 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 14, 14, 14, 36, 36, 49, 49, 36, 36, 68, 68, 49, 49, 1, 1, 1, 1, 10, 14, 36, 49, 68, 68, 68, 68, 68, 49, 1, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 37, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057046 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [48, 47, 48, 47, 48, 48, 43, 23, 22, 23, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 48, 48, 48, 48, 43, 22, 6, 1, 12, 12, 12, 12, 12, 1, 48, 48] 68
rigid atoms, others: [35, 12, 13, 14, 15, 16, 17, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 156
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057046 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 68, 46, 44, 41, 12, 12, 1, 1, 12, 12, 1, 1, 1, 1, 12, 12, 68, 68, 68, 68, 68, 42, 12, 12, 1, 1, 1, 1, 1, 12, 68, 68] 68
rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 213
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057046 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057046
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057046/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057046
Building REAL300000057047
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057047'
/scratch/stefan/7769638/working/building/REAL300000057047 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057047

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057047/0 /scratch/stefan/7769638/working/building/REAL300000057047 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 51)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/51
`/scratch/stefan/7769638/working/3D/51' -> `0.mol2'
Preparing input files

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

`REAL300000057047.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057047.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057047/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057047 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 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, 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
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 20, 20, 20, 20, 20, 16, 16, 16, 10, 7, 1, 1, 1, 1, 20, 20, 20, 20, 20] 20
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35])
total number of confs: 43
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057047 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 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, 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
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [10, 1, 10, 10, 16, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 10, 10, 10, 16, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1] 20
rigid atoms, others: [1, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 55
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057047 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057047
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057047/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057047
Building REAL300000057048
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057048'
/scratch/stefan/7769638/working/building/REAL300000057048 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057048

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057048/0 /scratch/stefan/7769638/working/building/REAL300000057048 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 52)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/52
`/scratch/stefan/7769638/working/3D/52' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CC(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1)

`REAL300000057048.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057048/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057048 none COC1=CC=C(CC(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 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
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, 1, 6, 20, 20, 20, 35, 35, 35, 85, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 35, 85, 85, 85, 85, 85, 1] 85
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 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: 253
number of broken/clashed sets: 84
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057048 none COC1=CC=C(CC(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 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
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, 85, 85, 38, 12, 12, 12, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 85, 85, 85, 85, 85, 85, 85, 38, 38, 12, 12, 12, 5, 3, 1, 1, 1, 1, 85] 85
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])
total number of confs: 214
number of broken/clashed sets: 84
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057048 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057048
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057048/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057048
Building REAL300000057049
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057049'
/scratch/stefan/7769638/working/building/REAL300000057049 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057049

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057049/0 /scratch/stefan/7769638/working/building/REAL300000057049 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 53)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/53
`/scratch/stefan/7769638/working/3D/53' -> `0.mol2'
Preparing input files

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

`REAL300000057049.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057049/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057049 none CC(C)(C)OC(=O)CCCC=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 91, 201, 39, 27, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 87, 43, 43, 27, 27, 5, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 725
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057049 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057049
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057049/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057049
Building REAL300000057050
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057050'
/scratch/stefan/7769638/working/building/REAL300000057050 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057050

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057050/0 /scratch/stefan/7769638/working/building/REAL300000057050 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 54)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/54
`/scratch/stefan/7769638/working/3D/54' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(C3=CC=CC(Cl)=C3)C2)C=C1)

`REAL300000057050.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057050.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057050/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057050 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(C3=CC=CC(Cl)=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 17, 17, 17, 26, 26, 26, 26, 26, 72, 72, 72, 72, 72, 72, 26, 1, 1, 1, 1, 8, 17, 26, 26, 26, 26, 26, 72, 72, 72, 72, 26, 26, 1, 1] 72
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057050 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(C3=CC=CC(Cl)=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [28, 25, 28, 25, 28, 28, 25, 7, 6, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 4, 7, 7, 7, 1, 28, 28, 28, 28, 25, 6, 1, 1, 1, 1, 1, 7, 7, 6, 7, 1, 1, 28, 28] 73
rigid atoms, others: [32, 33, 34, 39, 40, 10, 11, 12, 13, 14, 15, 16, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 41, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057050 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(C3=CC=CC(Cl)=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 73, 73, 73, 73, 25, 25, 25, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 73, 73, 73, 73, 73, 25, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 73, 73] 73
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 189
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057050 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057050
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057050/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057050
Building REAL300000057051
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057051'
/scratch/stefan/7769638/working/building/REAL300000057051 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057051

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057051/0 /scratch/stefan/7769638/working/building/REAL300000057051 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 55)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/55
`/scratch/stefan/7769638/working/3D/55' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057051.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057051/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057051 none NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 25, 26, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 5, 5, 1, 1, 8, 25, 46, 46, 46, 46, 46] 98
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 142
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057051 none NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 46, 98, 98, 46, 46, 46, 27, 27, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 98, 98, 46, 46, 27, 8, 6, 1, 1, 1, 1] 98
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: 307
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057051 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057051
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057051/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057051
Building REAL300000057052
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057052'
/scratch/stefan/7769638/working/building/REAL300000057052 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057052

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057052/0 /scratch/stefan/7769638/working/building/REAL300000057052 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 56)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/56
`/scratch/stefan/7769638/working/3D/56' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCOC1)

`REAL300000057052.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057052/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057052 none COC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 4, 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, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [84, 76, 39, 39, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 116, 116, 116, 116, 84, 84, 84, 76, 39, 17, 7, 1, 1, 1, 1, 116, 116, 116, 116, 116, 116, 116] 116
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, 38, 39, 40])
total number of confs: 380
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057052 none COC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 4, 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, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [19, 8, 1, 8, 37, 37, 64, 64, 64, 113, 116, 116, 113, 114, 116, 116, 116, 116, 1, 1, 1, 1, 1, 19, 19, 19, 8, 37, 64, 113, 116, 116, 116, 116, 1, 1, 1, 1, 1, 1, 1] 116
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 2, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 371
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057052 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057052
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057052/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057052
Building REAL300000057053
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057053'
/scratch/stefan/7769638/working/building/REAL300000057053 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057053

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057053/0 /scratch/stefan/7769638/working/building/REAL300000057053 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 57)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/57
`/scratch/stefan/7769638/working/3D/57' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@]1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[C@@H]1C1=CC=CC=C1)

`REAL300000057053.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057053.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057053/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057053 none C[C@]1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 12, 12, 35, 35, 35, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 12, 35, 64, 64, 64, 64, 64, 1, 1, 2, 2, 2, 2, 2] 64
rigid atoms, others: [0, 1, 2, 36, 37, 17, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42])
total number of confs: 181
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057053 none C[C@]1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [64, 20, 20, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 20, 12, 5, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64] 64
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057053 none C[C@]1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 12, 12, 35, 35, 35, 64, 64, 64, 64, 64, 64, 64, 64, 64, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 35, 64, 64, 64, 64, 64, 2, 2, 1, 1, 1, 1, 1] 64
rigid atoms, others: [38, 39, 40, 41, 42, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 175
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057053 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057053
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057053/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057053
Building REAL300000057054
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057054'
/scratch/stefan/7769638/working/building/REAL300000057054 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057054

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057054/0 /scratch/stefan/7769638/working/building/REAL300000057054 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 58)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/58
`/scratch/stefan/7769638/working/3D/58' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=C2C=CC(O)=C3F)C=C1)

`REAL300000057054.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057054.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057054/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057054 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=C2C=CC(O)=C3F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 1, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 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, 1, 1, 10, 18, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 10, 18, 20, 20, 20, 40, 1, 1] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33])
total number of confs: 91
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057054 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=C2C=CC(O)=C3F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 1, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 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, 20, 20, 19, 6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 19, 5, 1, 1, 1, 2, 20, 20] 40
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33, 35, 24, 25, 26, 27, 28, 29])
total number of confs: 51
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057054 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057054/1 /scratch/stefan/7769638/working/building/REAL300000057054 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 59)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/59
`/scratch/stefan/7769638/working/3D/59' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=C2C=CC([O-])=C3F)C=C1)

`REAL300000057054.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057054.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057054/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057054 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=C2C=CC([O-])=C3F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 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
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, 8, 18, 18, 18, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 8, 18, 22, 22, 22, 1, 1] 22
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057054 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=C2C=CC([O-])=C3F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 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
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, 21, 22, 22, 21, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 21, 7, 1, 1, 1, 22, 22] 22
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33, 24, 25, 26, 27, 28, 29])
total number of confs: 58
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057054 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057054
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057054/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057054/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057054
Building REAL300000057055
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057055'
/scratch/stefan/7769638/working/building/REAL300000057055 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057055

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057055/0 /scratch/stefan/7769638/working/building/REAL300000057055 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 60)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/60
`/scratch/stefan/7769638/working/3D/60' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN2CCCC2=C1)

`REAL300000057055.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057055/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057055 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN2CCCC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 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: [18, 18, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 22, 22, 22, 22, 22, 22, 22, 18, 18, 18, 10, 7, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22] 22
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 48
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057055 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN2CCCC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 11, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 11, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1] 22
rigid atoms, others: [1, 34, 35, 36, 37, 38, 33, 39, 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])
total number of confs: 65
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057055 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057055
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057055/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057055
Building REAL300000057056
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057056'
/scratch/stefan/7769638/working/building/REAL300000057056 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057056

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057056/0 /scratch/stefan/7769638/working/building/REAL300000057056 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 61)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/61
`/scratch/stefan/7769638/working/3D/61' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057056.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057056.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057056/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057056 none CC1=CC=CC=C1C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 1, 1, 5, 5, 5, 5, 5, 5, 22, 22, 43, 43, 43, 92, 92, 92, 92, 92, 92, 92, 92, 92, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 22, 43, 92, 92, 92, 92, 92] 92
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 33, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057056 none CC1=CC=CC=C1C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 53, 56, 56, 53, 53, 56, 56, 56, 56, 5, 5, 5, 5, 1, 5, 5, 1, 1, 1, 1, 10, 25, 53, 56, 56, 56, 56] 92
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 35, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057056 none CC1=CC=CC=C1C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [92, 92, 92, 56, 92, 92, 56, 56, 56, 56, 56, 56, 26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 92, 92, 92, 92, 56, 92, 92, 56, 56, 56, 56, 26, 14, 7, 1, 1, 1, 1] 92
rigid atoms, others: [42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 277
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057056 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057056
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057056/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057056
Building REAL300000057057
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057057'
/scratch/stefan/7769638/working/building/REAL300000057057 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057057

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057057/0 /scratch/stefan/7769638/working/building/REAL300000057057 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 62)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/62
`/scratch/stefan/7769638/working/3D/62' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=COC2=CC=CC=C12)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057057.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057057/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057057 none CC(CC1=COC2=CC=CC=C12)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 49, 49, 49, 124, 124, 124, 124, 124, 124, 124, 124, 124, 21, 21, 21, 7, 7, 1, 1, 1, 1, 1, 49, 124, 124, 124, 124, 124] 124
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 362
number of broken/clashed sets: 110
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057057 none CC(CC1=COC2=CC=CC=C12)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 56, 124, 124, 124, 124, 124, 124, 124, 124, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 19, 56, 56, 124, 124, 124, 124, 124, 5, 3, 1, 1, 1, 1] 124
rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 289
number of broken/clashed sets: 110
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057057 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057057
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057057/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057057
Building REAL300000057058
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057058'
/scratch/stefan/7769638/working/building/REAL300000057058 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057058

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057058/0 /scratch/stefan/7769638/working/building/REAL300000057058 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 63)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/63
`/scratch/stefan/7769638/working/3D/63' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(O)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1)

`REAL300000057058.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057058.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057058/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057058 none CC1=CC(O)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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]
1  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, 11, 11, 30, 30, 30, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 2, 2, 2, 1, 2, 11, 30, 55, 55, 55, 55, 55, 1] 110
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 36, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 163
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057058 none CC1=CC(O)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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]
1  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: [55, 44, 55, 55, 55, 28, 28, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 110, 28, 16, 7, 1, 1, 1, 1, 55] 110
rigid atoms, others: [32, 33, 34, 35, 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, 36])
total number of confs: 257
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057058 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057058
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057058/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057058
Building REAL300000057059
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057059'
/scratch/stefan/7769638/working/building/REAL300000057059 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057059

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057059/0 /scratch/stefan/7769638/working/building/REAL300000057059 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 64)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/64
`/scratch/stefan/7769638/working/3D/64' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN2C2CC2)C=C1)

`REAL300000057059.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057059/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057059 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN2C2CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 16, 16, 16, 45, 45, 86, 86, 86, 86, 86, 122, 122, 1, 1, 1, 1, 8, 16, 45, 86, 86, 86, 122, 122, 122, 122, 122, 1, 1] 122
rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 36, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 287
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057059 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN2C2CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 31, 30, 31, 10, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 71, 71, 71, 71, 71, 30, 10, 1, 1, 1, 7, 7, 7, 7, 7, 71, 71] 103
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057059 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN2C2CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [102, 102, 102, 102, 102, 102, 102, 58, 58, 58, 27, 27, 7, 7, 7, 7, 7, 1, 1, 1, 1, 102, 102, 102, 102, 102, 58, 27, 7, 7, 7, 1, 1, 1, 1, 1, 102, 102] 102
rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37])
total number of confs: 284
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057059 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057059
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057059/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057059
Building REAL300000057060
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057060'
/scratch/stefan/7769638/working/building/REAL300000057060 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057060

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057060/0 /scratch/stefan/7769638/working/building/REAL300000057060 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 65)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/65
`/scratch/stefan/7769638/working/3D/65' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C12CCC2)

`REAL300000057060.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057060/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057060 none COC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C12CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 7, 8, 8, 23, 24, 24, 23, 24, 24, 24, 24, 24, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 23, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1] 24
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 38, 40, 19, 20, 21, 22, 36, 26, 27, 28, 37, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 68
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057060 none COC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C12CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 7, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24] 24
rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38, 39, 40])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057060 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057060
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057060/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057060
Building REAL300000057061
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057061'
/scratch/stefan/7769638/working/building/REAL300000057061 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057061

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057061/0 /scratch/stefan/7769638/working/building/REAL300000057061 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 66)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/66
`/scratch/stefan/7769638/working/3D/66' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=NN1C)

`REAL300000057061.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057061.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057061/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057061 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [31, 31, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 31, 77, 77, 77, 97, 97, 77, 97, 97, 77, 77, 77, 31, 31, 31, 15, 7, 1, 1, 1, 1, 77, 97, 97, 77, 97, 97, 77, 77, 77] 97
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 231
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057061 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 1, 10, 10, 31, 31, 31, 71, 77, 77, 71, 71, 77, 77, 77, 77, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 1, 10, 10, 10, 31, 71, 77, 77, 77, 77, 1, 7, 7, 1, 7, 7, 2, 2, 2] 97
rigid atoms, others: [1, 37, 16, 17, 18, 19, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 261
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057061 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [39, 7, 39, 39, 60, 60, 60, 95, 97, 97, 95, 95, 97, 97, 97, 97, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 39, 39, 60, 95, 97, 97, 97, 97, 7, 1, 1, 1, 1, 1, 7, 7, 7] 97
rigid atoms, others: [38, 39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 284
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057061 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057061
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057061/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057061
Building REAL300000057062
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057062'
/scratch/stefan/7769638/working/building/REAL300000057062 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057062

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057062/0 /scratch/stefan/7769638/working/building/REAL300000057062 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 67)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/67
`/scratch/stefan/7769638/working/3D/67' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=C(F)C=C2)=N1)

`REAL300000057062.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057062.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057062/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057062 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=C(F)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 37, 37, 37, 110, 122, 122, 110, 117, 122, 122, 122, 122, 1, 1, 6, 6, 1, 2, 6, 6, 1, 2, 2, 2, 1, 11, 37, 110, 122, 122, 122, 122, 6, 6, 6, 6] 127
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 407
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057062 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=C(F)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [122, 122, 122, 55, 55, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 122, 122, 127, 127, 122, 127, 127, 127, 122, 122, 122, 122, 122, 55, 17, 7, 1, 1, 1, 1, 127, 127, 127, 127] 127
rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057062 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=C(F)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 20, 20, 52, 52, 52, 124, 127, 127, 124, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 20, 52, 124, 127, 127, 127, 127, 1, 1, 1, 1] 127
rigid atoms, others: [39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 360
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057062 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057062
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057062/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057062
Building REAL300000057063
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057063'
/scratch/stefan/7769638/working/building/REAL300000057063 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057063

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057063/0 /scratch/stefan/7769638/working/building/REAL300000057063 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 68)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/68
`/scratch/stefan/7769638/working/3D/68' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2OC(F)(F)O3)C=C1)

`REAL300000057063.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057063.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057063/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057063 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2OC(F)(F)O3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'F', 'F', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 7, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 16, 16, 16, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 9, 16, 34, 50, 50, 50, 1, 1] 50
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33])
total number of confs: 89
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057063 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2OC(F)(F)O3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'F', 'F', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 7, 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, 3, 7, 7, 7, 3, 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, 23, 23, 23, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 23, 13, 1, 1, 1, 51, 51] 51
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 137
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057063 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057063
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057063/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057063
Building REAL300000057064
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057064'
/scratch/stefan/7769638/working/building/REAL300000057064 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057064

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057064/0 /scratch/stefan/7769638/working/building/REAL300000057064 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 69)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/69
`/scratch/stefan/7769638/working/3D/69' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC1(C)C)

`REAL300000057064.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057064.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057064/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057064 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC1(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [54, 36, 36, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 60, 60, 60, 60, 54, 54, 54, 54, 54, 17, 7, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60] 65
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, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 252
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057064 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC1(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 1, 9, 9, 28, 28, 28, 60, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 28, 60, 60, 60, 60, 60, 1, 1, 1, 2, 2, 2, 2, 2, 2] 65
rigid atoms, others: [33, 34, 35, 2, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 209
number of broken/clashed sets: 35
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057064 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057064
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057064/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057064
Building REAL300000057065
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057065'
/scratch/stefan/7769638/working/building/REAL300000057065 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057065

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057065/0 /scratch/stefan/7769638/working/building/REAL300000057065 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 70)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/70
`/scratch/stefan/7769638/working/3D/70' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NN1C)

`REAL300000057065.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057065/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057065 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 2, 2, 2, 1, 7, 11, 29, 29, 29, 29, 29, 2, 2, 2] 29
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 89
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057065 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 24, 24, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 29, 29, 29, 29, 29, 29, 24, 8, 5, 1, 1, 1, 1, 29, 29, 29] 29
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 58
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057065 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057065
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057065/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057065
Building REAL300000057066
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057066'
/scratch/stefan/7769638/working/building/REAL300000057066 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057066

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057066/0 /scratch/stefan/7769638/working/building/REAL300000057066 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 71)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/71
`/scratch/stefan/7769638/working/3D/71' -> `0.mol2'
Preparing input files

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

`REAL300000057066.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057066.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057066/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057066 none CS(=O)(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 3, 3, 3, 1, 1, 1, 9, 17, 32, 32, 32, 32, 32, 1] 50
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 24, 38, 28, 29, 30] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057066 none CS(=O)(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 32, 50, 50, 32, 28, 32, 32, 24, 24, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 28, 32, 32, 24, 12, 7, 1, 1, 1, 1, 32] 50
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, 38])
total number of confs: 186
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057066 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057066
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057066/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057066
Building REAL300000057067
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057067'
/scratch/stefan/7769638/working/building/REAL300000057067 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057067

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057067/0 /scratch/stefan/7769638/working/building/REAL300000057067 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 72)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/72
`/scratch/stefan/7769638/working/3D/72' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1)

`REAL300000057067.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057067.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057067/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057067 none COC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 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, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 45, 45, 107, 109, 109, 108, 109, 109, 109, 109, 109, 1, 1, 1, 2, 2, 2, 1, 1, 9, 9, 9, 45, 107, 109, 109, 109, 109, 2, 2, 2, 1] 109
rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 22, 23, 24, 28, 29] set([0, 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: 298
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057067 none COC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 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, 7, 7, 4, 7, 6, 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]
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, 66, 61, 109, 109, 61, 61, 61, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 109, 109, 109, 109, 109, 109, 109, 109, 61, 61, 61, 16, 7, 1, 1, 1, 1, 109, 109, 109, 109] 109
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 365
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057067 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057067
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057067/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057067
Building REAL300000057068
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057068'
/scratch/stefan/7769638/working/building/REAL300000057068 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057068

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057068/0 /scratch/stefan/7769638/working/building/REAL300000057068 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 73)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/73
`/scratch/stefan/7769638/working/3D/73' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(N(C)C)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057068.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057068.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057068/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057068 none CC1=CC(N(C)C)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 1, 1, 1, 1, 13, 13, 25, 25, 25, 48, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 2, 1, 7, 7, 7, 7, 7, 7, 1, 1, 13, 25, 48, 48, 48, 48, 48] 50
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 35, 36, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 153
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057068 none CC1=CC(N(C)C)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [48, 48, 48, 34, 34, 50, 50, 48, 48, 29, 29, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 48, 48, 29, 13, 7, 1, 1, 1, 1] 50
rigid atoms, others: [40, 41, 42, 43, 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, 36, 37, 38, 39])
total number of confs: 161
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057068 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057068
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057068/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057068
Building REAL300000057069
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057069'
/scratch/stefan/7769638/working/building/REAL300000057069 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057069

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057069/0 /scratch/stefan/7769638/working/building/REAL300000057069 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 74)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/74
`/scratch/stefan/7769638/working/3D/74' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1)

`REAL300000057069.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057069/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057069 none CCC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 4, 4, 12, 13, 13, 31, 35, 35, 31, 33, 35, 35, 35, 35, 1, 1, 6, 6, 6, 6, 6, 1, 4, 12, 31, 35, 35, 35, 35, 1] 51
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 36, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 135
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057069 none CCC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 32, 32, 35, 35, 32, 32, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 51, 51, 51, 51, 51, 35, 32, 12, 7, 1, 1, 1, 1, 35] 51
rigid atoms, others: [32, 33, 34, 35, 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, 36])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057069 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057069
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057069/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057069
Building REAL300000057070
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057070'
/scratch/stefan/7769638/working/building/REAL300000057070 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057070

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057070/0 /scratch/stefan/7769638/working/building/REAL300000057070 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 75)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/75
`/scratch/stefan/7769638/working/3D/75' -> `0.mol2'
Preparing input files

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

`REAL300000057070.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057070.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057070/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057070 none CC(CCCCC#N)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 5, 5, 5, 5, 1, 8, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 111, 111, 157, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 111, 111, 133, 133, 154, 154, 201, 201, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 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])
total number of confs: 980
number of broken/clashed sets: 175
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057070 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057070
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057070/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057070
Building REAL300000057071
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057071'
/scratch/stefan/7769638/working/building/REAL300000057071 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057071

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057071/0 /scratch/stefan/7769638/working/building/REAL300000057071 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 76)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/76
`/scratch/stefan/7769638/working/3D/76' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)CN1C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057071.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057071.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057071/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057071 none CC(C)(C)OC(=O)CN1C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 51, 52, 52, 39, 6, 39, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 15, 15, 29, 33, 33, 29, 29, 33, 33, 33, 33, 52, 52, 52, 52, 52, 52, 52, 52, 52, 6, 6, 1, 1, 1, 6, 14, 29, 33, 33, 33, 33] 201
rigid atoms, others: [11, 39, 8, 9, 10, 7, 12, 13, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 246
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057071 none CC(C)(C)OC(=O)CN1C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
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, 192, 77, 192, 33, 33, 33, 33, 33, 11, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 33, 33, 33, 11, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [45, 46, 47, 48, 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, 40, 41, 42, 43, 44])
total number of confs: 586
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057071 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057071
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057071/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057071
Building REAL300000057072
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057072'
/scratch/stefan/7769638/working/building/REAL300000057072 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057072

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057072/0 /scratch/stefan/7769638/working/building/REAL300000057072 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 77)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/77
`/scratch/stefan/7769638/working/3D/77' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1CCCC(=O)N1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057072.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057072/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057072 none CC(CC1CCCC(=O)N1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 6, 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]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 17, 17, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 42, 42, 42, 42, 42] 42
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42])
total number of confs: 130
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057072 none CC(CC1CCCC(=O)N1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 6, 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]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 41, 42, 42, 42, 42, 42, 42, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 14, 14, 14, 41, 41, 42, 42, 42, 42, 42, 42, 42, 42, 5, 3, 1, 1, 1, 1] 42
rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 141
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057072 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057072
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057072/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057072
Building REAL300000057073
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057073'
/scratch/stefan/7769638/working/building/REAL300000057073 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057073

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057073/0 /scratch/stefan/7769638/working/building/REAL300000057073 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 78)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/78
`/scratch/stefan/7769638/working/3D/78' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CC(Cl)=C3C2)C=C1)

`REAL300000057073.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057073/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057073 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CC(Cl)=C3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 8, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1] 39
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 73
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057073 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CC(Cl)=C3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 39
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 23, 24, 25, 26, 27, 28])
total number of confs: 95
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057073 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057073
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057073/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057073
Building REAL300000057074
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057074'
/scratch/stefan/7769638/working/building/REAL300000057074 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057074

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057074/0 /scratch/stefan/7769638/working/building/REAL300000057074 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 79)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/79
`/scratch/stefan/7769638/working/3D/79' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCCC2)C=C1)

`REAL300000057074.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057074.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057074/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057074 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 42, 42, 105, 105, 105, 105, 105, 152, 152, 152, 152, 1, 1, 1, 1, 9, 15, 42, 105, 105, 152, 152, 152, 152, 152, 152, 152, 152, 152, 1, 1] 152
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 342
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057074 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 74, 74, 74, 72, 32, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 74, 74, 74, 74, 72, 32, 9, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 74, 74] 100
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 217
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057074 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [100, 100, 100, 100, 100, 100, 100, 66, 66, 66, 30, 30, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 66, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100] 100
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42])
total number of confs: 278
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057074 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057074
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057074/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057074
Building REAL300000057075
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057075'
/scratch/stefan/7769638/working/building/REAL300000057075 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057075

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057075/0 /scratch/stefan/7769638/working/building/REAL300000057075 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 80)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/80
`/scratch/stefan/7769638/working/3D/80' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC(F)=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057075.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057075.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057075/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057075 none CC1=NN(C2=CC=CC(F)=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 11, 11, 39, 39, 39, 87, 96, 96, 93, 96, 96, 96, 96, 96, 2, 2, 2, 7, 7, 6, 7, 1, 11, 39, 87, 96, 96, 96, 96] 149
rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 35] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 274
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057075 none CC1=NN(C2=CC=CC(F)=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 34, 80, 80, 80, 143, 149, 149, 149, 149, 149, 149, 149, 149, 7, 7, 7, 1, 1, 1, 1, 7, 34, 80, 143, 149, 149, 149, 149] 149
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 396
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057075 none CC1=NN(C2=CC=CC(F)=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 96, 96, 96, 149, 149, 149, 149, 149, 149, 96, 49, 49, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 149, 149, 149, 149, 96, 49, 16, 7, 1, 1, 1, 1] 149
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: 260
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057075 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057075
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057075/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057075
Building REAL300000057076
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057076'
/scratch/stefan/7769638/working/building/REAL300000057076 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057076

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057076/0 /scratch/stefan/7769638/working/building/REAL300000057076 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 81)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/81
`/scratch/stefan/7769638/working/3D/81' -> `0.mol2'
Preparing input files

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

`REAL300000057076.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057076.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057076/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057076 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 14, 7, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48] 48
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 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: 89
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057076 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 10, 24, 24, 24, 45, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 11, 11, 11, 23, 45, 48, 48, 48, 48, 1, 4, 4, 3, 4, 4] 48
rigid atoms, others: [1, 36, 16, 17, 18, 19, 20, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057076 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 3, 21, 21, 35, 35, 35, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 21, 21, 21, 35, 48, 48, 48, 48, 48, 3, 1, 1, 1, 1, 1] 48
rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 133
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057076 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057076
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057076/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057076
Building REAL300000057077
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057077'
/scratch/stefan/7769638/working/building/REAL300000057077 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057077

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057077/0 /scratch/stefan/7769638/working/building/REAL300000057077 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 82)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/82
`/scratch/stefan/7769638/working/3D/82' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OCCCCOC3=C2)C=C1)

`REAL300000057077.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057077.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057077/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057077 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OCCCCOC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 9
rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057077 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OCCCCOC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 12, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 29, 28, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48] 48
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 44, 43, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 131
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057077 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057077
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057077/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057077
Building REAL300000057078
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057078'
/scratch/stefan/7769638/working/building/REAL300000057078 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057078

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057078/0 /scratch/stefan/7769638/working/building/REAL300000057078 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 83)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/83
`/scratch/stefan/7769638/working/3D/83' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC(Br)=C2)C=C1)

`REAL300000057078.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057078.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057078/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057078 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC(Br)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 7, 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, 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, 9, 12, 12, 12, 24, 24, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 9, 12, 24, 51, 51, 51, 1, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057078 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC(Br)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 7, 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, 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, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 27, 7, 1, 1, 1, 51, 51] 51
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 135
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057078 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057078
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057078/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057078
Building REAL300000057079
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057079'
/scratch/stefan/7769638/working/building/REAL300000057079 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057079

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057079/0 /scratch/stefan/7769638/working/building/REAL300000057079 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 84)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/84
`/scratch/stefan/7769638/working/3D/84' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(F)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057079.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057079.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057079/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057079 none COC1=CC(F)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7, 7, 4, 7, 6, 4, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 36, 37, 37, 63, 69, 69, 63, 63, 69, 69, 69, 69, 1, 3, 3, 3, 1, 1, 10, 36, 63, 69, 69, 69, 69, 1] 69
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 23, 36, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 231
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057079 none COC1=CC(F)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7, 7, 4, 7, 6, 4, 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
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, 24, 24, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 69, 69, 69, 69, 69, 69, 24, 12, 7, 1, 1, 1, 1, 69] 69
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, 36])
total number of confs: 119
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057079 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057079
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057079/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057079
Building REAL300000057080
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057080'
/scratch/stefan/7769638/working/building/REAL300000057080 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057080

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057080/0 /scratch/stefan/7769638/working/building/REAL300000057080 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 85)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/85
`/scratch/stefan/7769638/working/3D/85' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)COC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057080.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057080.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057080/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057080 none CC(C)COC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 32, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 51, 68, 68, 56, 68, 68, 68, 68, 68, 44, 44, 44, 44, 44, 44, 44, 32, 32, 1, 1, 1, 1, 6, 20, 51, 68, 68, 68, 68] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 38, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 456
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057080 none CC(C)COC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [198, 201, 201, 156, 68, 68, 68, 35, 68, 68, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 68, 68, 68, 34, 16, 7, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 622
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057080 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057080
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057080/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057080
Building REAL300000057081
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057081'
/scratch/stefan/7769638/working/building/REAL300000057081 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057081

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057081/0 /scratch/stefan/7769638/working/building/REAL300000057081 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 86)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/86
`/scratch/stefan/7769638/working/3D/86' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC(Br)=CS1)

`REAL300000057081.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057081.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057081/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057081 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC(Br)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 17, 1, 14, 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, 2, 2, 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: [26, 26, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 33, 33, 33, 33, 33, 26, 26, 26, 12, 7, 1, 1, 1, 1, 33] 33
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 66
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057081 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC(Br)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 17, 1, 14, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [12, 1, 12, 12, 18, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 33, 33, 33, 33, 33, 1] 33
rigid atoms, others: [1, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 93
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057081 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057081
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057081/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057081
Building REAL300000057082
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057082'
/scratch/stefan/7769638/working/building/REAL300000057082 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057082

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057082/0 /scratch/stefan/7769638/working/building/REAL300000057082 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 87)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/87
`/scratch/stefan/7769638/working/3D/87' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=C(Cl)C=C3)C2)C=C1)

`REAL300000057082.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057082/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057082 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=C(Cl)C=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'Cl', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 16, 16, 16, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 10, 16, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1] 37
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 75
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057082 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=C(Cl)C=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'Cl', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 34, 37, 34, 37, 37, 31, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 37, 37, 37, 37, 31, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 37, 37] 37
rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 43, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 44, 45])
total number of confs: 116
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057082 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=C(Cl)C=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'Cl', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 16, 16, 16, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 37, 37, 37, 37, 35, 16, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 37, 37] 37
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, 43, 44, 45])
total number of confs: 97
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057082 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057082
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057082/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057082
Building REAL300000057083
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057083'
/scratch/stefan/7769638/working/building/REAL300000057083 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057083

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057083/0 /scratch/stefan/7769638/working/building/REAL300000057083 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 88)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/88
`/scratch/stefan/7769638/working/3D/88' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1OC(=O)CC)

`REAL300000057083.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057083.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057083/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057083 none CCOC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1OC(=O)CC 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.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.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 1, 1, 1, 1, 1, 7, 7, 8, 8, 8, 16, 18, 18, 16, 18, 18, 18, 18, 18, 1, 1, 1, 1, 7, 19, 19, 64, 24, 24, 24, 24, 24, 1, 7, 8, 16, 18, 18, 18, 18, 1, 1, 64, 64, 64, 64, 64] 201
rigid atoms, others: [34, 3, 4, 5, 6, 42, 43, 2, 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, 44, 45, 46, 47, 48])
total number of confs: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057083 none CCOC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1OC(=O)CC 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.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.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 18, 18, 18, 6, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 18, 71, 125, 125, 179, 87, 87, 87, 87, 87, 18, 6, 5, 5, 1, 1, 1, 1, 18, 18, 179, 179, 179, 179, 179] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 734
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057083 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057083
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057083/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057083
Building REAL300000057084
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057084'
/scratch/stefan/7769638/working/building/REAL300000057084 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057084

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057084/0 /scratch/stefan/7769638/working/building/REAL300000057084 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 89)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/89
`/scratch/stefan/7769638/working/3D/89' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057084.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057084.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057084/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057084 none CS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 1, 1, 1, 1, 1, 10, 10, 34, 35, 35, 71, 75, 75, 74, 74, 75, 75, 75, 75, 1, 7, 7, 7, 1, 1, 10, 34, 71, 75, 75, 75, 75] 94
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 236
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057084 none CS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [94, 75, 94, 94, 75, 75, 75, 34, 34, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 75, 94, 94, 94, 75, 75, 34, 10, 7, 1, 1, 1, 1] 94
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: 240
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057084 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057084
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057084/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057084
Building REAL300000057085
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057085'
/scratch/stefan/7769638/working/building/REAL300000057085 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057085

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057085/0 /scratch/stefan/7769638/working/building/REAL300000057085 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 90)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/90
`/scratch/stefan/7769638/working/3D/90' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1C(F)(F)F)

`REAL300000057085.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057085.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057085/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057085 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 20, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 6, 20, 47, 47, 47, 47, 47, 1, 1] 47
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 19, 20, 21, 22, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 141
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057085 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 24, 24, 9, 9, 6, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 47, 47, 24, 24, 47, 47, 47, 47, 47, 47, 47, 24, 9, 6, 1, 1, 1, 1, 47, 47] 47
rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 302
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057085 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057085
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057085/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057085
Building REAL300000057086
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057086'
/scratch/stefan/7769638/working/building/REAL300000057086 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057086

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057086/0 /scratch/stefan/7769638/working/building/REAL300000057086 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 91)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/91
`/scratch/stefan/7769638/working/3D/91' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057086.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057086.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057086/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057086 none CS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [6, 1, 6, 6, 1, 1, 1, 1, 1, 6, 6, 23, 24, 24, 55, 62, 62, 59, 60, 62, 62, 62, 62, 1, 7, 7, 7, 1, 1, 6, 23, 55, 62, 62, 62, 62] 80
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 215
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057086 none CS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [80, 62, 80, 80, 62, 62, 62, 33, 33, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 62, 80, 80, 80, 62, 62, 33, 10, 6, 1, 1, 1, 1] 80
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: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057086 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057086
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057086/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057086
Building REAL300000057087
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057087'
/scratch/stefan/7769638/working/building/REAL300000057087 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057087

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057087/0 /scratch/stefan/7769638/working/building/REAL300000057087 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 92)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/92
`/scratch/stefan/7769638/working/3D/92' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)[C@@H]1C[C@H]1C1=CC=CS1)

`REAL300000057087.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057087.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057087/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057087 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)[C@@H]1C[C@H]1C1=CC=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 35, 115, 115, 115, 115, 115, 171, 171, 171, 171, 35, 35, 35, 15, 7, 1, 1, 1, 1, 115, 115, 171, 171, 171] 171
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39])
total number of confs: 382
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057087 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)[C@@H]1C[C@H]1C1=CC=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 45, 45, 45, 104, 115, 115, 105, 110, 115, 115, 115, 115, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 11, 11, 11, 45, 104, 115, 115, 115, 115, 1, 1, 12, 12, 12] 171
rigid atoms, others: [1, 35, 36, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 371
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057087 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)[C@@H]1C[C@H]1C1=CC=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [70, 12, 70, 70, 114, 114, 114, 169, 171, 171, 171, 171, 171, 171, 171, 171, 12, 12, 12, 1, 12, 1, 1, 1, 1, 1, 70, 70, 70, 114, 169, 171, 171, 171, 171, 12, 12, 1, 1, 1] 171
rigid atoms, others: [37, 38, 39, 19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 475
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057087 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057087
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057087/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057087
Building REAL300000057088
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057088'
/scratch/stefan/7769638/working/building/REAL300000057088 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057088

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057088/0 /scratch/stefan/7769638/working/building/REAL300000057088 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 93)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/93
`/scratch/stefan/7769638/working/3D/93' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CC=C2CCCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1)

`REAL300000057088.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057088.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057088/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057088 none NC1=CC=C2CCCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['N.pl3', '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.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']
dock atom type numbers: [8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 6, 7, 7, 18, 19, 19, 18, 19, 19, 19, 19, 19, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18, 19, 19, 19, 19, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44] set([38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057088 none NC1=CC=C2CCCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['N.pl3', '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.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']
dock atom type numbers: [8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 6, 1, 1, 1, 1, 19] 19
rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 40
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057088 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057088
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057088/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057088
Building REAL300000057089
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057089'
/scratch/stefan/7769638/working/building/REAL300000057089 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057089

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057089/0 /scratch/stefan/7769638/working/building/REAL300000057089 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 94)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/94
`/scratch/stefan/7769638/working/3D/94' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1CC2CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C1C2)

`REAL300000057089.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057089/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057089 none COC(=O)C1CC2CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C1C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 24, 24, 24, 24, 24, 1, 1, 1] 27
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 40, 42, 41, 23, 24, 28, 29, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38, 39])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057089 none COC(=O)C1CC2CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C1C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 24, 27, 24, 24, 24, 24, 24, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 24, 27, 27, 27, 24, 24, 24, 24, 24, 24, 12, 7, 1, 1, 1, 1, 24, 24, 24] 27
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, 42])
total number of confs: 66
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057089 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057089
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057089/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057089
Building REAL300000057090
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057090'
/scratch/stefan/7769638/working/building/REAL300000057090 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057090

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057090/0 /scratch/stefan/7769638/working/building/REAL300000057090 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 95)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/95
`/scratch/stefan/7769638/working/3D/95' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3CC3)=C2)C=C1)

`REAL300000057090.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057090.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057090/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057090 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3CC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 18, 18, 18, 44, 44, 98, 98, 44, 98, 98, 133, 133, 98, 1, 1, 1, 1, 8, 18, 44, 98, 98, 72, 133, 133, 133, 133, 133, 98, 1, 1] 133
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 477
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057090 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3CC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [92, 79, 92, 79, 92, 92, 79, 35, 34, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 92, 92, 92, 92, 79, 34, 11, 1, 1, 1, 7, 7, 7, 7, 7, 1, 92, 92] 127
rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 335
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057090 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3CC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [127, 125, 127, 125, 127, 127, 125, 73, 73, 73, 40, 40, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 127, 127, 127, 127, 125, 73, 40, 7, 7, 7, 1, 1, 1, 1, 1, 7, 127, 127] 127
rigid atoms, others: [32, 33, 34, 35, 36, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 362
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057090 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057090
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057090/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057090
Building REAL300000057091
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057091'
/scratch/stefan/7769638/working/building/REAL300000057091 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057091

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057091/0 /scratch/stefan/7769638/working/building/REAL300000057091 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 96)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/96
`/scratch/stefan/7769638/working/3D/96' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CN=C3CC2)C=C1)

`REAL300000057091.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057091.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057091/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057091 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CN=C3CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 13, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 8, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 41, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 65
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057091 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CN=C3CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 34, 35, 34, 35, 35, 34, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 35
rigid atoms, others: [10, 11, 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, 40, 41, 23, 24, 25, 26, 27, 28])
total number of confs: 92
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057091 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057091
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057091/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057091
Building REAL300000057092
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057092'
/scratch/stefan/7769638/working/building/REAL300000057092 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057092

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057092/0 /scratch/stefan/7769638/working/building/REAL300000057092 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 97)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/97
`/scratch/stefan/7769638/working/3D/97' -> `0.mol2'
Preparing input files

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

`REAL300000057092.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057092.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057092/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057092 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 16, 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, 2, 2, 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
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 43, 43, 43, 43, 43, 43, 20, 20, 20, 14, 7, 1, 1, 1, 1, 43, 43, 43] 43
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 89
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057092 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 16, 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, 2, 2, 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
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, 25, 25, 25, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 25, 43, 43, 43, 43, 43, 1, 1, 1] 43
rigid atoms, others: [32, 1, 34, 33, 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])
total number of confs: 115
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057092 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057092
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057092/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057092
Building REAL300000057093
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057093'
/scratch/stefan/7769638/working/building/REAL300000057093 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057093

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057093/0 /scratch/stefan/7769638/working/building/REAL300000057093 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 98)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/98
`/scratch/stefan/7769638/working/3D/98' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(CC)C(=O)NCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057093.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057093.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057093/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057093 none CCC1(CC)C(=O)NCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 23, 26, 26, 23, 23, 26, 26, 26, 26, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 8, 23, 26, 26, 26, 26] 26
rigid atoms, others: [1, 2, 3, 36, 5, 6, 7, 8, 9, 10, 39, 12, 11, 35, 38, 37] set([0, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45])
total number of confs: 103
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057093 none CCC1(CC)C(=O)NCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 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]
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, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 7, 1, 1, 1, 1] 26
rigid atoms, others: [42, 43, 44, 45, 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, 36, 37, 38, 39, 40, 41])
total number of confs: 57
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057093 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057093
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057093/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057093
Building REAL300000057094
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057094'
/scratch/stefan/7769638/working/building/REAL300000057094 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057094

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057094/0 /scratch/stefan/7769638/working/building/REAL300000057094 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 99)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/99
`/scratch/stefan/7769638/working/3D/99' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1CC1=CC=CC=C1)

`REAL300000057094.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057094.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057094/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057094 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 34, 35, 35, 74, 77, 77, 76, 76, 77, 77, 77, 77, 1, 1, 1, 1, 6, 13, 13, 8, 13, 13, 2, 2, 2, 1, 11, 34, 74, 77, 77, 77, 77, 2, 2, 2, 6, 6, 13, 13, 13, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 4, 32, 19, 20, 21, 22] set([5, 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, 48, 49])
total number of confs: 275
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057094 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 77, 25, 25, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 155, 201, 201, 201, 201, 201, 77, 77, 77, 77, 25, 11, 7, 1, 1, 1, 1, 77, 77, 77, 155, 155, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 614
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057094 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 12, 12, 12, 62, 63, 121, 121, 121, 199, 201, 201, 201, 201, 201, 201, 201, 201, 12, 13, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 12, 62, 121, 199, 201, 201, 201, 201, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1] 201
rigid atoms, others: [45, 46, 47, 48, 49, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 613
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057094 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057094
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057094/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057094
Building REAL300000057095
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057095'
/scratch/stefan/7769638/working/building/REAL300000057095 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057095

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057095/0 /scratch/stefan/7769638/working/building/REAL300000057095 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 100)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/100
`/scratch/stefan/7769638/working/3D/100' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C)

`REAL300000057095.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057095/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057095 none CC(C)(C)OC(=O)NC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 31, 36, 36, 12, 7, 12, 1, 1, 1, 1, 1, 1, 9, 10, 10, 32, 40, 40, 32, 37, 40, 40, 40, 40, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 1, 1, 1, 9, 32, 40, 40, 40, 40, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [11, 38, 7, 8, 9, 10, 39, 12, 40, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 244
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057095 none CC(C)(C)OC(=O)NC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 162, 112, 162, 40, 40, 40, 40, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 40, 40, 40, 13, 7, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40] 201
rigid atoms, others: [43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52])
total number of confs: 545
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057095 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057095
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057095/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057095
Building REAL300000057096
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057096'
/scratch/stefan/7769638/working/building/REAL300000057096 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057096

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057096/0 /scratch/stefan/7769638/working/building/REAL300000057096 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 101)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/101
`/scratch/stefan/7769638/working/3D/101' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC[NH+](CCO)CC2)C=C1)

`REAL300000057096.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057096/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057096 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[NH+](CCO)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 6, 7, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 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
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, 4, 5, 5, 5, 7, 7, 7, 7, 7, 7, 11, 11, 7, 7, 1, 1, 1, 1, 4, 5, 7, 7, 7, 7, 11, 11, 11, 11, 33, 7, 7, 7, 7, 1, 1] 33
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 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, 35, 36, 37, 38, 39, 40])
total number of confs: 78
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057096 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[NH+](CCO)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 6, 7, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 1, 1, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 3, 3, 5, 5, 15, 1, 1, 1, 1, 7, 7] 33
rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 55
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057096 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057096
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057096/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057096
Building REAL300000057097
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057097'
/scratch/stefan/7769638/working/building/REAL300000057097 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057097

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057097/0 /scratch/stefan/7769638/working/building/REAL300000057097 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 102)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/102
`/scratch/stefan/7769638/working/3D/102' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCO[C@@H]1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)[C@]12CCCO2)

`REAL300000057097.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057097.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057097/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057097 none CCO[C@@H]1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)[C@]12CCCO2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 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, 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, 3, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 26, 30, 30, 29, 29, 30, 30, 30, 30, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 9, 26, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1] 30
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 41, 42, 39, 44, 43, 40, 21, 22, 23, 24, 25, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057097 none CCO[C@@H]1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)[C@]12CCCO2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 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, 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, 11, 11, 6, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 6, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30] 30
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44])
total number of confs: 58
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057097 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057097
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057097/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057097
Building REAL300000057098
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057098'
/scratch/stefan/7769638/working/building/REAL300000057098 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057098

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057098/0 /scratch/stefan/7769638/working/building/REAL300000057098 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 103)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/103
`/scratch/stefan/7769638/working/3D/103' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057098.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057098/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057098 none CC1=NN(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 25, 26, 26, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 2, 2, 2, 2, 2, 2, 10, 25, 58, 58, 58, 58, 58, 1] 58
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 21] set([7, 8, 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: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057098 none CC1=NN(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 57, 32, 32, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 58, 58, 58, 58, 58, 58, 58, 32, 11, 7, 1, 1, 1, 1, 58] 58
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 109
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057098 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057098
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057098/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057098
Building REAL300000057099
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057099'
/scratch/stefan/7769638/working/building/REAL300000057099 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057099

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057099/0 /scratch/stefan/7769638/working/building/REAL300000057099 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 104)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/104
`/scratch/stefan/7769638/working/3D/104' -> `0.mol2'
Preparing input files

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

`REAL300000057099.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057099/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057099 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Cl)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Cl', '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, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 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]
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: [18, 18, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 43, 43, 43, 43, 43, 43, 43, 18, 18, 18, 12, 7, 1, 1, 1, 1, 43, 43, 43, 86] 86
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 169
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057099 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Cl)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Cl', '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, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 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]
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, 21, 21, 21, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 43, 43, 43, 43, 43, 1, 1, 1, 2] 86
rigid atoms, others: [1, 34, 35, 33, 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, 36])
total number of confs: 117
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057099 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057099/1 /scratch/stefan/7769638/working/building/REAL300000057099 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 105)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/105
`/scratch/stefan/7769638/working/3D/105' -> `1.mol2'
Preparing input files

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

`REAL300000057099.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057099/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057099 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Cl)C=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Cl', '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, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 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, 2, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 22, 22, 7, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 37, 37, 37, 37, 37, 37, 37, 32, 32, 32, 22, 7, 1, 1, 1, 1, 37, 37, 37] 37
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 81
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057099 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Cl)C=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Cl', '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, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 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, 2, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 35, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 35, 37, 37, 37, 37, 1, 1, 1] 37
rigid atoms, others: [1, 34, 35, 33, 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])
total number of confs: 99
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057099 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057099
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057099/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057099/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057099
Building REAL300000057100
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057100'
/scratch/stefan/7769638/working/building/REAL300000057100 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057100

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057100/0 /scratch/stefan/7769638/working/building/REAL300000057100 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 106)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/106
`/scratch/stefan/7769638/working/3D/106' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057100.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057100.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057100/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057100 none CCN1C=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 1, 1, 6, 16, 37, 37, 37, 37, 37] 63
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 131
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057100 none CCN1C=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 37, 37, 37, 37, 37, 26, 26, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 63, 63, 63, 63, 63, 37, 37, 26, 12, 7, 1, 1, 1, 1] 63
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 234
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057100 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057100
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057100/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057100
Building REAL300000057101
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057101'
/scratch/stefan/7769638/working/building/REAL300000057101 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057101

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057101/0 /scratch/stefan/7769638/working/building/REAL300000057101 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 107)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/107
`/scratch/stefan/7769638/working/3D/107' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC(O)=CC=C32)C=C1)

`REAL300000057101.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057101.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057101/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057101 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC(O)=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 11, 8, 8, 1, 5, 5, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 7, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 7, 9, 15, 15, 15, 15, 15, 30, 15, 15, 1, 1] 30
rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 67
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057101 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC(O)=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 11, 8, 8, 1, 5, 5, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 8, 1, 1, 1, 1, 1, 2, 1, 1, 17, 17] 34
rigid atoms, others: [32, 33, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 38, 23, 24, 25, 26, 27, 28, 37])
total number of confs: 45
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057101 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057101
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057101/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057101
Building REAL300000057102
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057102'
/scratch/stefan/7769638/working/building/REAL300000057102 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057102

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057102/0 /scratch/stefan/7769638/working/building/REAL300000057102 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 108)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/108
`/scratch/stefan/7769638/working/3D/108' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Cl)=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057102.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057102/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057102 none COC1=CC(Cl)=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 16, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 37, 37, 37, 91, 95, 95, 95, 95, 95, 95, 95, 95, 4, 4, 4, 1, 1, 1, 10, 10, 10, 37, 91, 95, 95, 95, 95] 95
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 250
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057102 none COC1=CC(Cl)=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 16, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 89, 95, 95, 95, 37, 37, 37, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 94, 95, 37, 37, 37, 16, 7, 1, 1, 1, 1] 95
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])
total number of confs: 186
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057102 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057102
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057102/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057102
Building REAL300000057103
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057103'
/scratch/stefan/7769638/working/building/REAL300000057103 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057103

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057103/0 /scratch/stefan/7769638/working/building/REAL300000057103 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 109)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/109
`/scratch/stefan/7769638/working/3D/109' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CC=C(F)C=C1Cl)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057103.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057103.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057103/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057103 none CC(CC1=CC=C(F)C=C1Cl)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 31, 31, 31, 67, 67, 67, 67, 67, 67, 67, 67, 67, 17, 17, 17, 5, 5, 1, 1, 1, 31, 67, 67, 67, 67, 67] 67
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 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])
total number of confs: 212
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057103 none CC(CC1=CC=C(F)C=C1Cl)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 49, 67, 67, 49, 59, 67, 67, 67, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 15, 15, 15, 49, 49, 67, 67, 67, 5, 3, 1, 1, 1, 1] 67
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])
total number of confs: 257
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057103 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057103
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057103/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057103
Building REAL300000057104
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057104'
/scratch/stefan/7769638/working/building/REAL300000057104 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057104

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057104/0 /scratch/stefan/7769638/working/building/REAL300000057104 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 110)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/110
`/scratch/stefan/7769638/working/3D/110' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NSC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057104.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057104.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057104/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057104 none COC1=NSC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 2, 2, 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, 8, 8, 21, 21, 21, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 3, 3, 3, 8, 20, 51, 51, 51, 51, 51, 1] 55
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 21] set([0, 7, 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: 139
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057104 none COC1=NSC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 2, 2, 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, 51, 51, 51, 51, 32, 32, 13, 13, 5, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 51, 55, 55, 55, 32, 13, 5, 1, 1, 1, 1, 51] 55
rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 32, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057104 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057104
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057104/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057104
Building REAL300000057105
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057105'
/scratch/stefan/7769638/working/building/REAL300000057105 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057105

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057105/0 /scratch/stefan/7769638/working/building/REAL300000057105 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 111)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/111
`/scratch/stefan/7769638/working/3D/111' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3NC(=O)NC3=C2)C=C1)

`REAL300000057105.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057105.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057105/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057105 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3NC(=O)NC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 10, 10, 10, 26, 26, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 8, 10, 26, 45, 45, 45, 45, 45, 1, 1] 45
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: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057105 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3NC(=O)NC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 20, 7, 1, 1, 1, 1, 1, 45, 45] 45
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057105 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057105
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057105/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057105
Building REAL300000057106
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057106'
/scratch/stefan/7769638/working/building/REAL300000057106 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057106

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057106/0 /scratch/stefan/7769638/working/building/REAL300000057106 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 112)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/112
`/scratch/stefan/7769638/working/3D/112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CNC(=O)C3=CC=CC=C32)C=C1)

`REAL300000057106.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057106.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057106/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057106 none O=C([O-])C1=CC=C(NC(=O)NN=C2CNC(=O)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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
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, 9, 13, 13, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 9, 13, 24, 24, 24, 24, 24, 24, 24, 1, 1] 24
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: 58
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057106 none O=C([O-])C1=CC=C(NC(=O)NN=C2CNC(=O)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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
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, 24, 9, 8, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 24, 24] 24
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 37, 36])
total number of confs: 65
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057106 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057106
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057106/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057106
Building REAL300000057107
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057107'
/scratch/stefan/7769638/working/building/REAL300000057107 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057107

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057107/0 /scratch/stefan/7769638/working/building/REAL300000057107 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 113)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/113
`/scratch/stefan/7769638/working/3D/113' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC3=CC=C([N+](=O)[O-])C=C32)C=C1)

`REAL300000057107.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057107.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057107/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057107 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC3=CC=C([N+](=O)[O-])C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 5, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1] 14
rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 30
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057107 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC3=CC=C([N+](=O)[O-])C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 7, 6, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 14
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 43, 44, 26, 27, 28, 29, 30, 31])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057107 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057107
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057107/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057107
Building REAL300000057108
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057108'
/scratch/stefan/7769638/working/building/REAL300000057108 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057108

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057108/0 /scratch/stefan/7769638/working/building/REAL300000057108 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 114)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/114
`/scratch/stefan/7769638/working/3D/114' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC1(C)C)

`REAL300000057108.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057108.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057108/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057108 none CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [93, 82, 42, 42, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 87, 87, 87, 87, 93, 93, 93, 93, 93, 82, 82, 16, 7, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 87, 87, 87] 109
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 470
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057108 none CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [29, 21, 8, 1, 8, 8, 29, 29, 29, 73, 87, 87, 73, 80, 87, 87, 87, 87, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 21, 21, 29, 73, 87, 87, 87, 87, 1, 1, 1, 2, 2, 2, 2, 2, 2] 109
rigid atoms, others: [3, 36, 37, 38, 18, 19, 20, 21, 22] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44])
total number of confs: 416
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057108 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057108
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057108/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057108
Building REAL300000057109
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057109'
/scratch/stefan/7769638/working/building/REAL300000057109 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057109

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057109/0 /scratch/stefan/7769638/working/building/REAL300000057109 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 115)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/115
`/scratch/stefan/7769638/working/3D/115' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F)

`REAL300000057109.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057109.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057109/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057109 none N#CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 19, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 6, 19, 47, 47, 47, 47, 47, 1] 47
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 21, 22, 23, 24, 25] set([32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057109 none N#CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 26, 26, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 47, 47, 47, 47, 47, 26, 10, 6, 1, 1, 1, 1, 47] 47
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057109 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057109
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057109/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057109
Building REAL300000057110
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057110'
/scratch/stefan/7769638/working/building/REAL300000057110 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057110

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057110/0 /scratch/stefan/7769638/working/building/REAL300000057110 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 116)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/116
`/scratch/stefan/7769638/working/3D/116' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1)

`REAL300000057110.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057110.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057110/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057110 none COC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 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, 7, 4, 7, 6, 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
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 45, 45, 45, 112, 116, 116, 114, 116, 116, 116, 116, 116, 1, 1, 1, 3, 3, 3, 1, 1, 10, 10, 10, 45, 112, 116, 116, 116, 116, 1] 116
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 22, 23, 24, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 333
number of broken/clashed sets: 68
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057110 none COC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 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, 7, 4, 7, 6, 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
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [116, 97, 84, 116, 116, 62, 62, 62, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 116, 116, 116, 62, 62, 62, 18, 7, 1, 1, 1, 1, 116] 116
rigid atoms, others: [35, 36, 37, 38, 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, 39])
total number of confs: 330
number of broken/clashed sets: 68
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057110 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057110
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057110/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057110
Building REAL300000057111
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057111'
/scratch/stefan/7769638/working/building/REAL300000057111 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057111

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057111/0 /scratch/stefan/7769638/working/building/REAL300000057111 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 117)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/117
`/scratch/stefan/7769638/working/3D/117' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OC(F)(F)OC3=C2)C=C1)

`REAL300000057111.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057111.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057111/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057111 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OC(F)(F)OC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 1, 1, 7, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 7, 11, 27, 49, 49, 49, 1, 1] 49
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057111 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OC(F)(F)OC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 1, 1, 7, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 22, 21, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 21, 6, 1, 1, 1, 49, 49] 49
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 133
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057111 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057111
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057111/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057111
Building REAL300000057112
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057112'
/scratch/stefan/7769638/working/building/REAL300000057112 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057112

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057112/0 /scratch/stefan/7769638/working/building/REAL300000057112 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 118)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/118
`/scratch/stefan/7769638/working/3D/118' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057112.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057112.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057112/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057112 none COC(=O)CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [52, 52, 9, 52, 1, 1, 1, 1, 1, 1, 9, 10, 10, 23, 30, 30, 23, 23, 30, 30, 30, 30, 1, 52, 52, 52, 9, 9, 1, 1, 1, 9, 23, 30, 30, 30, 30, 1, 1] 120
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 38, 28, 29, 30, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057112 none COC(=O)CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 73, 120, 30, 30, 30, 30, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 120, 120, 120, 73, 73, 30, 30, 30, 8, 6, 1, 1, 1, 1, 30, 30] 120
rigid atoms, others: [33, 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, 37, 38])
total number of confs: 392
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057112 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057112
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057112/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057112
Building REAL300000057113
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057113'
/scratch/stefan/7769638/working/building/REAL300000057113 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057113

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057113/0 /scratch/stefan/7769638/working/building/REAL300000057113 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 119)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/119
`/scratch/stefan/7769638/working/3D/119' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H]1C[C@H]2CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C[C@H]2C1)

`REAL300000057113.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057113.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057113/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057113 none CO[C@H]1C[C@H]2CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C[C@H]2C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 5, 7, 7, 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, 7, 7, 7, 4, 7, 6, 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]
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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 33, 37, 37, 33, 33, 37, 37, 37, 37, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 1, 9, 33, 37, 37, 37, 37, 1, 1, 1, 1] 37
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 30, 31, 32, 33, 40, 41, 42, 43] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057113 none CO[C@H]1C[C@H]2CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C[C@H]2C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 5, 7, 7, 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, 7, 7, 7, 4, 7, 6, 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]
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, 37, 37, 37, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 7, 1, 1, 1, 1, 37, 37, 37, 37] 37
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, 42, 43])
total number of confs: 71
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057113 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057113
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057113/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057113
Building REAL300000057114
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057114'
/scratch/stefan/7769638/working/building/REAL300000057114 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057114

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057114/0 /scratch/stefan/7769638/working/building/REAL300000057114 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 120)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/120
`/scratch/stefan/7769638/working/3D/120' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1)

`REAL300000057114.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057114.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057114/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057114 none CC1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 7, 7, 22, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 2, 2, 2, 1, 7, 22, 40, 40, 40, 40, 40, 1] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 21, 22, 23, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057114 none CC1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [30, 30, 40, 40, 40, 30, 30, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 30, 14, 7, 1, 1, 1, 1, 40] 40
rigid atoms, others: [32, 33, 34, 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, 35])
total number of confs: 162
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057114 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057114
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057114/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057114
Building REAL300000057115
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057115'
/scratch/stefan/7769638/working/building/REAL300000057115 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057115

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057115/0 /scratch/stefan/7769638/working/building/REAL300000057115 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 121)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/121
`/scratch/stefan/7769638/working/3D/121' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC(=O)C=C2)C=C1)

`REAL300000057115.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057115.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057115/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057115 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC(=O)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 11, 8, 8, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 10, 12, 12, 12, 25, 25, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 10, 12, 25, 41, 41, 41, 41, 1, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057115 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC(=O)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 11, 8, 8, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 19, 18, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 18, 8, 1, 1, 1, 1, 41, 41] 41
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 113
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057115 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057115
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057115/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057115
Building REAL300000057116
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057116'
/scratch/stefan/7769638/working/building/REAL300000057116 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057116

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057116/0 /scratch/stefan/7769638/working/building/REAL300000057116 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 122)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/122
`/scratch/stefan/7769638/working/3D/122' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057116.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057116.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057116/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057116 none CN(C)C(=O)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', '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.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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 31, 32, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 17, 31, 32, 32, 32, 32] 40
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 35] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 111
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057116 none CN(C)C(=O)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', '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.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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 32, 40, 32, 32, 32, 32, 32, 16, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 40, 40, 40, 32, 32, 32, 32, 16, 6, 6, 1, 1, 1, 1] 40
rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 88
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057116 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057116
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057116/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057116
Building REAL300000057117
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057117'
/scratch/stefan/7769638/working/building/REAL300000057117 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057117

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057117/0 /scratch/stefan/7769638/working/building/REAL300000057117 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 123)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/123
`/scratch/stefan/7769638/working/3D/123' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC2=C1C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CC2)

`REAL300000057117.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057117.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057117/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057117 none CC1=CC=CC2=C1C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 5, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 2, 2, 2, 1, 1, 1, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 22, 23, 36, 27, 28, 29, 37] set([32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057117 none CC1=CC=CC2=C1C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 14, 7, 1, 1, 1, 1, 18, 18, 18, 18] 18
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057117 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057117
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057117/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057117
Building REAL300000057118
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057118'
/scratch/stefan/7769638/working/building/REAL300000057118 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057118

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057118/0 /scratch/stefan/7769638/working/building/REAL300000057118 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 124)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/124
`/scratch/stefan/7769638/working/3D/124' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=C1OCO2)

`REAL300000057118.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057118.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057118/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057118 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=C1OCO2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [31, 31, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 54, 54, 54, 54, 54, 54, 54, 54, 31, 31, 31, 16, 7, 1, 1, 1, 1, 54, 54, 54, 54, 54] 54
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 103
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057118 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=C1OCO2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 1, 12, 12, 31, 31, 31, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 31, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1] 54
rigid atoms, others: [1, 34, 35, 36, 37, 38, 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])
total number of confs: 139
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057118 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057118
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057118/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057118
Building REAL300000057119
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057119'
/scratch/stefan/7769638/working/building/REAL300000057119 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057119

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057119/0 /scratch/stefan/7769638/working/building/REAL300000057119 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 125)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/125
`/scratch/stefan/7769638/working/3D/125' -> `0.mol2'
Preparing input files

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

`REAL300000057119.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057119.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057119/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057119 none COCCC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)NC(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 45, 38, 16, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 56, 94, 94, 117, 117, 117, 117, 62, 62, 62, 45, 44, 40, 40, 16, 8, 5, 5, 1, 1, 1, 1, 56, 117, 117, 117, 117, 117, 117, 117, 117, 117] 201
rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 515
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057119 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057119
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057119/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057119
Building REAL300000057120
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057120'
/scratch/stefan/7769638/working/building/REAL300000057120 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057120

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057120/0 /scratch/stefan/7769638/working/building/REAL300000057120 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 126)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/126
`/scratch/stefan/7769638/working/3D/126' -> `0.mol2'
Preparing input files

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

`REAL300000057120.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057120.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057120/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057120 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 12, 1, 12, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
260  conformations in input
total number of sets (complete confs): 260
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 65, 65, 65, 65, 65, 65, 65, 65, 27, 27, 27, 13, 7, 1, 1, 1, 1, 65, 65, 65, 65, 130, 130, 65] 260
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 373
number of broken/clashed sets: 196
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057120 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 12, 1, 12, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
260  conformations in input
total number of sets (complete confs): 260
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 36, 36, 36, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 36, 65, 65, 65, 65, 65, 1, 2, 2, 2, 2, 2, 1] 260
rigid atoms, others: [1, 34, 40, 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, 35, 36, 37, 38, 39])
total number of confs: 191
number of broken/clashed sets: 196
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057120 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057120
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057120/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057120
Building REAL300000057121
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057121'
/scratch/stefan/7769638/working/building/REAL300000057121 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057121

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057121/0 /scratch/stefan/7769638/working/building/REAL300000057121 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 127)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/127
`/scratch/stefan/7769638/working/3D/127' -> `0.mol2'
Preparing input files

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

`REAL300000057121.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057121.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057121/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057121 none COC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [60, 58, 28, 28, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 62, 62, 62, 60, 60, 60, 58, 28, 14, 7, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 62, 62, 62] 62
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 209
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057121 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057121
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057121/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057121
Building REAL300000057122
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057122'
/scratch/stefan/7769638/working/building/REAL300000057122 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057122

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057122/0 /scratch/stefan/7769638/working/building/REAL300000057122 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 128)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/128
`/scratch/stefan/7769638/working/3D/128' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCO[C@@H]1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)[C@H]1OC)

`REAL300000057122.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057122.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057122/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057122 none CCO[C@@H]1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)[C@H]1OC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 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, 2, 2, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [10, 7, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 36, 45, 45, 36, 41, 45, 45, 45, 45, 1, 1, 1, 6, 10, 10, 10, 10, 10, 1, 1, 9, 36, 45, 45, 45, 45, 6, 6, 6] 77
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057122 none CCO[C@@H]1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)[C@H]1OC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 7, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 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, 2, 2, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 71, 45, 45, 45, 45, 45, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 45, 45, 63, 77, 77, 77, 77, 77, 45, 45, 17, 7, 1, 1, 1, 1, 63, 63, 63] 77
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057122 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057122
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057122/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057122
Building REAL300000057123
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057123'
/scratch/stefan/7769638/working/building/REAL300000057123 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057123

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057123/0 /scratch/stefan/7769638/working/building/REAL300000057123 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 129)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/129
`/scratch/stefan/7769638/working/3D/129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1=CC=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1)

`REAL300000057123.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057123/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057123 none CSC1=CC=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', '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.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']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 31, 38, 38, 31, 31, 38, 38, 38, 38, 1, 1, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 38, 38, 38, 38, 1] 62
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 43] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 37, 38, 39, 40, 41, 42])
total number of confs: 153
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057123 none CSC1=CC=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', '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.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']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 38, 38, 38, 38, 38, 38, 38, 38, 38, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 62, 62, 62, 38, 38, 38, 38, 38, 38, 38, 38, 16, 7, 1, 1, 1, 1, 38] 62
rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 122
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057123 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057123
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057123/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057123
Building REAL300000057124
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057124'
/scratch/stefan/7769638/working/building/REAL300000057124 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057124

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057124/0 /scratch/stefan/7769638/working/building/REAL300000057124 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 130)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/130
`/scratch/stefan/7769638/working/3D/130' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN2CCCCC2=C1)

`REAL300000057124.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057124.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057124/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057124 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN2CCCCC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [18, 18, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 22, 22, 22, 22, 22, 22, 22, 22, 18, 18, 18, 10, 7, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 22
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 48
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057124 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN2CCCCC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 5, 5, 9, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 22
rigid atoms, others: [1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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])
total number of confs: 69
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057124 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057124
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057124/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057124
Building REAL300000057125
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057125'
/scratch/stefan/7769638/working/building/REAL300000057125 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057125

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057125/0 /scratch/stefan/7769638/working/building/REAL300000057125 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 131)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/131
`/scratch/stefan/7769638/working/3D/131' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCN1C(=O)OC(C)(C)C)

`REAL300000057125.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057125.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057125/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057125 none CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 45, 45, 37, 41, 45, 45, 45, 45, 1, 1, 1, 1, 5, 5, 16, 20, 20, 20, 2, 2, 2, 1, 1, 1, 9, 37, 45, 45, 45, 45, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20] 163
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 40, 41, 42, 43, 18, 19, 20, 21, 5, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 204
number of broken/clashed sets: 89
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057125 none CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [45, 45, 45, 45, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 45, 45, 45, 106, 106, 163, 163, 163, 163, 45, 45, 45, 45, 45, 45, 14, 7, 1, 1, 1, 1, 45, 45, 45, 45, 163, 163, 163, 163, 163, 163, 163, 163, 163] 163
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 370
number of broken/clashed sets: 89
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057125 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057125
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057125/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057125
Building REAL300000057126
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057126'
/scratch/stefan/7769638/working/building/REAL300000057126 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057126

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057126/0 /scratch/stefan/7769638/working/building/REAL300000057126 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 132)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/132
`/scratch/stefan/7769638/working/3D/132' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(F)(F)CC2)C=C1)

`REAL300000057126.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057126.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057126/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057126 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(F)(F)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', '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, 11, 8, 8, 1, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 8, 15, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1] 29
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 20, 21, 22, 23] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 66
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057126 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(F)(F)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', '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, 11, 8, 8, 1, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30] 30
rigid atoms, others: [32, 33, 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, 8, 9, 34, 35, 20, 21, 22, 23, 24, 25])
total number of confs: 71
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057126 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057126
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057126/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057126
Building REAL300000057127
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057127'
/scratch/stefan/7769638/working/building/REAL300000057127 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057127

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057127/0 /scratch/stefan/7769638/working/building/REAL300000057127 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 133)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/133
`/scratch/stefan/7769638/working/3D/133' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=CC=N2)C=C1)

`REAL300000057127.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057127/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057127 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 5, 5, 5, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 3, 5, 6, 10, 10, 10, 10, 10, 10, 1, 1] 10
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: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057127 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 5, 3, 1, 1, 2, 2, 2, 2, 10, 10] 10
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 30
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057127 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 4, 4, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 6, 4, 2, 2, 1, 1, 1, 1, 10, 10] 10
rigid atoms, others: [33, 34, 35, 36, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 29
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057127 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057127
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057127/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057127
Building REAL300000057128
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057128'
/scratch/stefan/7769638/working/building/REAL300000057128 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057128

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057128/0 /scratch/stefan/7769638/working/building/REAL300000057128 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 134)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/134
`/scratch/stefan/7769638/working/3D/134' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C2=NN(C)C=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057128.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057128.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057128/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057128 none CC1=CC=C(C2=NN(C)C=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 21, 21, 34, 34, 34, 64, 65, 65, 65, 65, 65, 65, 65, 65, 1, 2, 2, 2, 1, 1, 8, 8, 8, 8, 21, 34, 64, 65, 65, 65, 65] 65
rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 189
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057128 none CC1=CC=C(C2=NN(C)C=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 51, 57, 57, 54, 54, 57, 57, 57, 57, 8, 8, 8, 8, 8, 8, 2, 2, 2, 1, 10, 22, 51, 57, 57, 57, 57] 65
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057128 none CC1=CC=C(C2=NN(C)C=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 65, 57, 57, 57, 57, 57, 57, 33, 33, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 57, 57, 57, 57, 33, 12, 7, 1, 1, 1, 1] 65
rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 113
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057128 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057128
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057128/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057128
Building REAL300000057129
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057129'
/scratch/stefan/7769638/working/building/REAL300000057129 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057129

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057129/0 /scratch/stefan/7769638/working/building/REAL300000057129 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 135)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/135
`/scratch/stefan/7769638/working/3D/135' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C2CCCCN2N=C1)

`REAL300000057129.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057129/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057129 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C2CCCCN2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [29, 29, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 45, 45, 45, 45, 45, 45, 45, 45, 29, 29, 29, 12, 7, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45] 45
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 77
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057129 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C2CCCCN2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 1, 10, 10, 24, 25, 25, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 24, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1] 45
rigid atoms, others: [1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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])
total number of confs: 133
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057129 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057129
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057129/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057129
Building REAL300000057130
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057130'
/scratch/stefan/7769638/working/building/REAL300000057130 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057130

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057130/0 /scratch/stefan/7769638/working/building/REAL300000057130 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 136)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/136
`/scratch/stefan/7769638/working/3D/136' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057130.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057130.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057130/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057130 none COC1=CC=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 9, 9, 20, 21, 21, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 2, 2, 2, 1, 1, 9, 20, 44, 44, 44, 44, 44] 44
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057130 none COC1=CC=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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, 26, 26, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 44, 44, 44, 44, 44, 44, 26, 11, 7, 1, 1, 1, 1] 44
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057130 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057130
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057130/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057130
Building REAL300000057131
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057131'
/scratch/stefan/7769638/working/building/REAL300000057131 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057131

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057131/0 /scratch/stefan/7769638/working/building/REAL300000057131 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 137)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/137
`/scratch/stefan/7769638/working/3D/137' -> `0.mol2'
Preparing input files

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

`REAL300000057131.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057131/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057131 none CC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)NC(=O)OC(C)(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [46, 16, 16, 7, 7, 6, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 102, 133, 133, 160, 160, 160, 160, 46, 46, 46, 46, 16, 7, 6, 1, 1, 1, 1, 102, 160, 160, 160, 160, 160, 160, 160, 160, 160] 160
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, 42, 43, 44, 45])
total number of confs: 495
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057131 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057131
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057131/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057131
Building REAL300000057132
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057132'
/scratch/stefan/7769638/working/building/REAL300000057132 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057132

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057132/0 /scratch/stefan/7769638/working/building/REAL300000057132 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 138)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/138
`/scratch/stefan/7769638/working/3D/138' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1OC2(CC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CC[NH+](C)CC2)

`REAL300000057132.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057132.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057132/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057132 none CC1OC2(CC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CC[NH+](C)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 39, 40, 41, 42, 46, 47, 48, 49] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 33, 34, 35, 36, 37, 38, 43, 44, 45])
total number of confs: 59
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057132 none CC1OC2(CC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CC[NH+](C)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 9, 6, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 6, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17
rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 35
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057132 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057132
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057132/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057132
Building REAL300000057133
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057133'
/scratch/stefan/7769638/working/building/REAL300000057133 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057133

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057133/0 /scratch/stefan/7769638/working/building/REAL300000057133 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 139)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/139
`/scratch/stefan/7769638/working/3D/139' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCN(C(=O)OCC3=CC=CC=C3)C2)C=C1)

`REAL300000057133.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057133/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057133 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCN(C(=O)OCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 7, 7, 7, 22, 22, 22, 22, 22, 32, 32, 62, 201, 201, 201, 201, 201, 201, 22, 1, 1, 1, 1, 6, 7, 22, 22, 22, 22, 201, 201, 201, 201, 201, 201, 201, 22, 22, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 47, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 660
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057133 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCN(C(=O)OCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 21, 15, 21, 21, 14, 7, 6, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 41, 68, 68, 41, 68, 68, 1, 21, 21, 21, 21, 14, 6, 1, 1, 1, 1, 41, 41, 68, 68, 45, 68, 68, 1, 1, 21, 21] 201
rigid atoms, others: [33, 34, 35, 36, 44, 10, 11, 12, 13, 14, 15, 16, 45, 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, 37, 38, 39, 40, 41, 42, 43, 46, 47])
total number of confs: 337
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057133 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCN(C(=O)OCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 201, 191, 122, 122, 122, 68, 68, 68, 68, 68, 49, 22, 49, 4, 1, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 191, 122, 68, 68, 68, 68, 4, 4, 1, 1, 1, 1, 1, 68, 68, 201, 201] 201
rigid atoms, others: [39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47])
total number of confs: 628
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057133 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057133
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057133/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057133
Building REAL300000057134
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057134'
/scratch/stefan/7769638/working/building/REAL300000057134 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057134

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057134/0 /scratch/stefan/7769638/working/building/REAL300000057134 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 140)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/140
`/scratch/stefan/7769638/working/3D/140' -> `0.mol2'
Preparing input files

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

`REAL300000057134.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057134/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057134 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 8, 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, 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
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 9, 9, 6, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 21, 21, 21, 21, 21, 21, 17, 17, 17, 9, 6, 1, 1, 1, 1, 21, 21, 21] 21
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 47
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057134 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 8, 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, 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
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [10, 1, 10, 10, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 18, 21, 21, 21, 21, 21, 1, 1, 1] 21
rigid atoms, others: [32, 1, 34, 33, 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])
total number of confs: 51
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057134 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057134
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057134/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057134
Building REAL300000057135
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057135'
/scratch/stefan/7769638/working/building/REAL300000057135 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057135

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057135/0 /scratch/stefan/7769638/working/building/REAL300000057135 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 141)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/141
`/scratch/stefan/7769638/working/3D/141' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(OC)=C1O)

`REAL300000057135.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057135.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057135/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057135 none COC1=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(OC)=C1O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
320  conformations in input
total number of sets (complete confs): 320
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 12, 58, 59, 59, 137, 150, 150, 145, 150, 150, 150, 150, 150, 1, 1, 1, 3, 1, 1, 3, 3, 3, 1, 13, 13, 13, 58, 137, 150, 150, 150, 150, 1, 3, 3, 3, 2] 320
rigid atoms, others: [1, 2, 3, 4, 5, 40, 21, 22, 23, 25, 26, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 420
number of broken/clashed sets: 214
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057135 none COC1=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(OC)=C1O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
284  conformations in input
total number of sets (complete confs): 284
using faster count positions algorithm for large data
unique positions, atoms: [142, 123, 123, 123, 60, 60, 60, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 123, 123, 123, 142, 123, 123, 142, 142, 142, 123, 60, 60, 60, 17, 7, 1, 1, 1, 1, 123, 142, 142, 142, 246] 284
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44])
total number of confs: 521
number of broken/clashed sets: 176
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057135 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057135
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057135/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057135
Building REAL300000057136
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057136'
/scratch/stefan/7769638/working/building/REAL300000057136 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057136

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057136/0 /scratch/stefan/7769638/working/building/REAL300000057136 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 142)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/142
`/scratch/stefan/7769638/working/3D/142' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@H+](CC3=CC=CC=C3)C3(CC3)C2)C=C1)

`REAL300000057136.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057136/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057136 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@H+](CC3=CC=CC=C3)C3(CC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 8, 8, 8, 24, 24, 24, 24, 24, 24, 30, 30, 30, 30, 30, 30, 24, 24, 24, 24, 1, 1, 1, 1, 6, 8, 24, 24, 24, 24, 30, 30, 30, 30, 30, 30, 30, 24, 24, 24, 24, 24, 24, 1, 1] 30
rigid atoms, others: [1, 3, 4, 5, 6, 7, 51, 52, 28, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 81
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057136 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@H+](CC3=CC=CC=C3)C3(CC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 21, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 3, 5, 5, 1, 1, 1, 1, 24, 24, 24, 24, 21, 9, 1, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 1, 1, 1, 1, 1, 1, 24, 24] 30
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 34, 35, 36, 37, 45, 46, 47, 48, 49, 50] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 51, 52])
total number of confs: 82
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057136 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@H+](CC3=CC=CC=C3)C3(CC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 28, 15, 15, 15, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 30, 30, 30, 30, 28, 15, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 30, 30] 30
rigid atoms, others: [40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 89
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057136 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057136/1 /scratch/stefan/7769638/working/building/REAL300000057136 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 143)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/143
`/scratch/stefan/7769638/working/3D/143' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@@H+](CC3=CC=CC=C3)C3(CC3)C2)C=C1)

`REAL300000057136.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057136/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057136 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@@H+](CC3=CC=CC=C3)C3(CC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 9, 9, 9, 23, 23, 23, 23, 23, 23, 29, 29, 29, 29, 29, 29, 23, 23, 23, 23, 1, 1, 1, 1, 6, 9, 23, 23, 23, 23, 29, 29, 29, 29, 29, 29, 29, 23, 23, 23, 23, 23, 23, 1, 1] 29
rigid atoms, others: [1, 3, 4, 5, 6, 7, 51, 52, 28, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 83
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057136 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@@H+](CC3=CC=CC=C3)C3(CC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [24, 21, 24, 21, 24, 24, 21, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 1, 1, 24, 24, 24, 24, 21, 9, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 24, 24] 30
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 34, 35, 36, 37, 45, 46, 47, 48, 49, 50] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 51, 52])
total number of confs: 97
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057136 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[N@@H+](CC3=CC=CC=C3)C3(CC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 28, 30, 28, 30, 30, 28, 15, 15, 15, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 30, 30, 30, 30, 28, 15, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 30, 30] 30
rigid atoms, others: [40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 103
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057136 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057136
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057136/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057136/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057136
Building REAL300000057137
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057137'
/scratch/stefan/7769638/working/building/REAL300000057137 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057137

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057137/0 /scratch/stefan/7769638/working/building/REAL300000057137 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 144)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/144
`/scratch/stefan/7769638/working/3D/144' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(CC(C)C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000057137.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057137.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057137/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057137 none COC1=CC=C(C(CC(C)C)=NNC(=O)NC2=CC=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.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 11, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 22, 24, 24, 10, 10, 36, 36, 36, 97, 108, 108, 104, 108, 108, 108, 108, 108, 1, 1, 2, 2, 2, 1, 1, 22, 22, 24, 24, 24, 24, 24, 24, 24, 36, 97, 108, 108, 108, 108, 1, 1] 112
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 48, 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, 46])
total number of confs: 372
number of broken/clashed sets: 68
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057137 none COC1=CC=C(C(CC(C)C)=NNC(=O)NC2=CC=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.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 11, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [108, 54, 54, 108, 108, 54, 54, 54, 93, 99, 99, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 108, 108, 93, 93, 99, 99, 99, 99, 99, 99, 99, 15, 7, 1, 1, 1, 1, 108, 108] 112
rigid atoms, others: [43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
total number of confs: 624
number of broken/clashed sets: 68
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057137 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057137
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057137/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057137
Building REAL300000057138
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057138'
/scratch/stefan/7769638/working/building/REAL300000057138 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057138

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057138/0 /scratch/stefan/7769638/working/building/REAL300000057138 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 145)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/145
`/scratch/stefan/7769638/working/3D/145' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CN1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057138.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057138.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057138/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057138 none CC(C)CN1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [6, 3, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 33, 34, 34, 69, 74, 74, 71, 74, 74, 74, 74, 74, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 1, 8, 33, 69, 74, 74, 74, 74] 113
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057138 none CC(C)CN1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 74, 74, 74, 74, 74, 31, 31, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 113, 113, 113, 113, 113, 113, 113, 113, 113, 74, 74, 31, 13, 7, 1, 1, 1, 1] 113
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 342
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057138 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057138
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057138/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057138
Building REAL300000057139
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057139'
/scratch/stefan/7769638/working/building/REAL300000057139 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057139

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057139/0 /scratch/stefan/7769638/working/building/REAL300000057139 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 146)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/146
`/scratch/stefan/7769638/working/3D/146' -> `0.mol2'
Preparing input files

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

`REAL300000057139.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057139.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057139/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057139 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Br)=CN=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 17, 1, 8, 1, 16, 1, 1, 7, 7, 6, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 26, 26, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 8, 12, 26, 32, 32, 1, 1] 32
rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057139 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Br)=CN=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 17, 1, 8, 1, 16, 1, 1, 7, 7, 6, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 18, 18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 18, 8, 1, 1, 32, 32] 32
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057139 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057139
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057139/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057139
Building REAL300000057140
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057140'
/scratch/stefan/7769638/working/building/REAL300000057140 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057140

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057140/0 /scratch/stefan/7769638/working/building/REAL300000057140 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 147)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/147
`/scratch/stefan/7769638/working/3D/147' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1CCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057140.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057140/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057140 none CCCC1CCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 34, 46, 46, 34, 39, 46, 46, 46, 46, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 34, 46, 46, 46, 46] 70
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 36, 38, 37, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44])
total number of confs: 216
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057140 none CCCC1CCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 46, 46, 46, 46, 46, 46, 46, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 70, 70, 70, 70, 70, 70, 70, 46, 46, 46, 46, 46, 46, 46, 46, 46, 16, 7, 1, 1, 1, 1] 70
rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 213
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057140 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057140
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057140/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057140
Building REAL300000057141
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057141'
/scratch/stefan/7769638/working/building/REAL300000057141 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057141

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057141/0 /scratch/stefan/7769638/working/building/REAL300000057141 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 148)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/148
`/scratch/stefan/7769638/working/3D/148' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC2=C1NC(=O)C2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057141.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057141.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057141/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057141 none COC1=CC=CC2=C1NC(=O)C2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 27, 34, 34, 28, 33, 34, 34, 34, 34, 3, 3, 3, 1, 1, 1, 1, 5, 27, 34, 34, 34, 34] 34
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057141 none COC1=CC=CC2=C1NC(=O)C2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 34, 34, 34, 34, 21, 21, 6, 21, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 34, 34, 34, 34, 34, 34, 34, 21, 6, 1, 1, 1, 1] 34
rigid atoms, others: [35, 36, 37, 38, 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])
total number of confs: 81
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057141 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057141
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057141/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057141
Building REAL300000057142
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057142'
/scratch/stefan/7769638/working/building/REAL300000057142 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057142

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057142/0 /scratch/stefan/7769638/working/building/REAL300000057142 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 149)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/149
`/scratch/stefan/7769638/working/3D/149' -> `0.mol2'
Preparing input files

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

`REAL300000057142.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057142.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057142/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057142 none CCOC(=O)C1=NNC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 12, 1, 11, 1, 8, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [26, 15, 8, 1, 8, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 56, 66, 66, 63, 63, 66, 66, 66, 66, 1, 27, 27, 27, 26, 26, 1, 7, 25, 56, 66, 66, 66, 66, 1] 132
rigid atoms, others: [3, 5, 6, 7, 8, 9, 24, 38, 30] set([0, 1, 2, 4, 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])
total number of confs: 284
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057142 none CCOC(=O)C1=NNC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 12, 1, 11, 1, 8, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [132, 126, 121, 66, 121, 66, 66, 66, 32, 32, 8, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 132, 132, 132, 132, 132, 66, 32, 8, 7, 1, 1, 1, 1, 66] 132
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, 38])
total number of confs: 318
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057142 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057142
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057142/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057142
Building REAL300000057143
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057143'
/scratch/stefan/7769638/working/building/REAL300000057143 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057143

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057143/0 /scratch/stefan/7769638/working/building/REAL300000057143 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 150)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/150
`/scratch/stefan/7769638/working/3D/150' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CCCCC1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057143.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057143/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057143 none CCC1CCCCC1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 30, 30, 62, 67, 67, 62, 62, 67, 67, 67, 67, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 62, 67, 67, 67, 67] 67
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 36, 33, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 220
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057143 none CCC1CCCCC1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 39, 39, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 39, 17, 7, 1, 1, 1, 1] 67
rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 167
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057143 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057143
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057143/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057143
Building REAL300000057144
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057144'
/scratch/stefan/7769638/working/building/REAL300000057144 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057144

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057144/0 /scratch/stefan/7769638/working/building/REAL300000057144 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 151)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/151
`/scratch/stefan/7769638/working/3D/151' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC2C=CC1CC2)

`REAL300000057144.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057144.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057144/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057144 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC2C=CC1CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [21, 21, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 23, 23, 23, 23, 23, 23, 23, 21, 21, 21, 12, 7, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 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: 61
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057144 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC2C=CC1CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 23
rigid atoms, others: [1, 34, 35, 36, 37, 38, 33, 40, 41, 42, 39, 43, 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])
total number of confs: 63
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057144 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057144
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057144/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057144
Building REAL300000057145
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057145'
/scratch/stefan/7769638/working/building/REAL300000057145 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057145

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057145/0 /scratch/stefan/7769638/working/building/REAL300000057145 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 152)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/152
`/scratch/stefan/7769638/working/3D/152' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=C2C=CC=C3[N+](=O)[O-])C=C1)

`REAL300000057145.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057145/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057145 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=C2C=CC=C3[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 8, 14, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19
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: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057145 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=C2C=CC=C3[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19
rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 22, 23, 24, 25, 26, 27, 28, 29, 37])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057145 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057145
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057145/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057145
Building REAL300000057146
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057146'
/scratch/stefan/7769638/working/building/REAL300000057146 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057146

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057146/0 /scratch/stefan/7769638/working/building/REAL300000057146 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 153)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/153
`/scratch/stefan/7769638/working/3D/153' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN1)

`REAL300000057146.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057146.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057146/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057146 none COC(=O)C1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [8, 8, 1, 8, 1, 1, 1, 1, 1, 11, 11, 28, 28, 28, 54, 62, 62, 58, 62, 62, 62, 62, 62, 1, 1, 8, 8, 8, 2, 2, 2, 11, 28, 54, 62, 62, 62, 62, 1, 1] 86
rigid atoms, others: [2, 4, 5, 6, 7, 8, 39, 23, 24, 38] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 208
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057146 none COC(=O)C1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [86, 86, 62, 86, 62, 62, 62, 35, 35, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 86, 86, 86, 62, 62, 62, 35, 12, 7, 1, 1, 1, 1, 62, 62] 86
rigid atoms, others: [34, 35, 36, 37, 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, 38, 39])
total number of confs: 194
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057146 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057146
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057146/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057146
Building REAL300000057147
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057147'
/scratch/stefan/7769638/working/building/REAL300000057147 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057147

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057147/0 /scratch/stefan/7769638/working/building/REAL300000057147 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 154)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/154
`/scratch/stefan/7769638/working/3D/154' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C=CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057147.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057147.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057147/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057147 none COC(=O)C=CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 11, 35, 11, 1, 1, 1, 1, 1, 1, 6, 6, 22, 23, 23, 71, 78, 78, 71, 76, 78, 78, 78, 78, 1, 36, 36, 36, 11, 11, 1, 1, 6, 22, 71, 78, 78, 78, 78] 178
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 25, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057147 none COC(=O)C=CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [178, 178, 115, 178, 115, 78, 78, 78, 78, 42, 42, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 178, 178, 178, 115, 115, 78, 78, 42, 12, 7, 1, 1, 1, 1] 178
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])
total number of confs: 495
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057147 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057147
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057147/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057147
Building REAL300000057148
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057148'
/scratch/stefan/7769638/working/building/REAL300000057148 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057148

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057148/0 /scratch/stefan/7769638/working/building/REAL300000057148 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 155)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/155
`/scratch/stefan/7769638/working/3D/155' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1O)

`REAL300000057148.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057148.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057148/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057148 none CCC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 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: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 8, 13, 29, 29, 29, 29, 29, 2] 102
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22, 23, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 94
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057148 none CCC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7]
1  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [51, 29, 29, 28, 29, 29, 25, 25, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 29, 51, 51, 51, 51, 51, 29, 29, 29, 25, 15, 7, 1, 1, 1, 1, 58] 102
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 261
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057148 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057148
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057148/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057148
Building REAL300000057149
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057149'
/scratch/stefan/7769638/working/building/REAL300000057149 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057149

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057149/0 /scratch/stefan/7769638/working/building/REAL300000057149 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 156)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/156
`/scratch/stefan/7769638/working/3D/156' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C2=NC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)S2)C=C1C)

`REAL300000057149.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057149.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057149/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057149 none CC1=CC=C(C2=NC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)S2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 5, 5, 5, 5, 9, 9, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 2, 2, 2, 1, 1, 5, 8, 13, 21, 21, 21, 21, 21, 1, 2, 2, 2] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 41, 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, 42, 43, 44])
total number of confs: 70
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057149 none CC1=CC=C(C2=NC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)S2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 8, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 4, 8, 13, 13, 13, 13, 13, 5, 5, 5, 5] 21
rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057149 none CC1=CC=C(C2=NC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)S2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 13, 13, 9, 9, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 21, 21, 21, 21, 21, 21, 21, 21, 13, 9, 5, 3, 1, 1, 1, 1, 21, 21, 21, 21] 21
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44])
total number of confs: 47
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057149 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057149
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057149/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057149
Building REAL300000057150
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057150'
/scratch/stefan/7769638/working/building/REAL300000057150 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057150

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057150/0 /scratch/stefan/7769638/working/building/REAL300000057150 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 157)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/157
`/scratch/stefan/7769638/working/3D/157' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057150.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057150.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057150/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057150 none CC(C)(C)OC(=O)NC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [38, 29, 38, 38, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 33, 47, 47, 33, 33, 47, 47, 47, 47, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 1, 1, 1, 1, 1, 1, 1, 9, 33, 47, 47, 47, 47, 1, 1] 201
rigid atoms, others: [11, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 51, 52, 43, 41, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48, 49, 50])
total number of confs: 295
number of broken/clashed sets: 141
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057150 none CC(C)(C)OC(=O)NC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 201, 201, 201, 147, 103, 147, 47, 47, 47, 47, 47, 47, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 47, 47, 47, 47, 47, 47, 47, 16, 7, 1, 1, 1, 1, 47, 47] 201
rigid atoms, others: [49, 50, 47, 48, 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, 43, 44, 45, 46, 51, 52])
total number of confs: 531
number of broken/clashed sets: 141
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057150 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057150
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057150/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057150
Building REAL300000057151
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057151'
/scratch/stefan/7769638/working/building/REAL300000057151 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057151

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057151/0 /scratch/stefan/7769638/working/building/REAL300000057151 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 158)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/158
`/scratch/stefan/7769638/working/3D/158' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)[C@H]2CCC[C@H]21)

`REAL300000057151.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057151.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057151/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057151 none CC1(C)C(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)[C@H]2CCC[C@H]21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 59
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057151 none CC1(C)C(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)[C@H]2CCC[C@H]21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 7, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19] 19
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 46
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057151 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057151
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057151/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057151
Building REAL300000057152
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057152'
/scratch/stefan/7769638/working/building/REAL300000057152 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057152

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057152/0 /scratch/stefan/7769638/working/building/REAL300000057152 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 159)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/159
`/scratch/stefan/7769638/working/3D/159' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC=C2F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057152.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057152.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057152/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057152 none CC1=NN(C2=CC=CC=C2F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 8, 1, 1, 1, 12, 12, 35, 36, 36, 89, 102, 102, 98, 102, 102, 102, 102, 102, 2, 2, 2, 7, 7, 7, 7, 1, 12, 35, 89, 102, 102, 102, 102] 127
rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 35] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 293
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057152 none CC1=NN(C2=CC=CC=C2F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 39, 72, 73, 73, 123, 127, 127, 127, 127, 127, 127, 127, 127, 8, 8, 8, 1, 1, 1, 1, 7, 40, 73, 123, 127, 127, 127, 127] 127
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057152 none CC1=NN(C2=CC=CC=C2F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [102, 102, 102, 102, 102, 127, 127, 127, 127, 127, 127, 102, 46, 46, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 102, 102, 102, 127, 127, 127, 127, 102, 46, 14, 7, 1, 1, 1, 1] 127
rigid atoms, others: [39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 213
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057152 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057152
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057152/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057152
Building REAL300000057153
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057153'
/scratch/stefan/7769638/working/building/REAL300000057153 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057153

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057153/0 /scratch/stefan/7769638/working/building/REAL300000057153 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 160)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/160
`/scratch/stefan/7769638/working/3D/160' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC=C2Cl)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057153.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057153.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057153/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057153 none CC1=NN(C2=CC=CC=C2Cl)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 12, 1, 1, 1, 8, 8, 32, 33, 33, 76, 88, 88, 83, 88, 88, 88, 88, 88, 2, 2, 2, 11, 11, 11, 11, 1, 8, 32, 76, 88, 88, 88, 88] 201
rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 35] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057153 none CC1=NN(C2=CC=CC=C2Cl)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 43, 43, 109, 109, 109, 191, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 12, 1, 1, 1, 1, 11, 43, 109, 191, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057153 none CC1=NN(C2=CC=CC=C2Cl)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 88, 201, 201, 201, 201, 201, 201, 88, 47, 47, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 88, 88, 88, 201, 201, 201, 201, 88, 47, 14, 7, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 320
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057153 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057153
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057153/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057153
Building REAL300000057154
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057154'
/scratch/stefan/7769638/working/building/REAL300000057154 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057154

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057154/0 /scratch/stefan/7769638/working/building/REAL300000057154 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 161)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/161
`/scratch/stefan/7769638/working/3D/161' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=C(C)C=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057154.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057154.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057154/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057154 none CC1=NN(C2=CC=C(C)C=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 3, 3, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 3, 7, 13, 13, 13, 13, 13] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 36, 38, 37, 31] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057154 none CC1=NN(C2=CC=C(C)C=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 3, 3, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 3, 6, 13, 13, 13, 13, 13] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 36, 38, 37, 31] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057154 none CC1=NN(C2=CC=C(C)C=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 9, 9, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 5, 3, 1, 1, 1, 1] 13
rigid atoms, others: [42, 43, 44, 45, 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, 40, 41])
total number of confs: 29
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057154 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057154
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057154/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057154
Building REAL300000057155
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057155'
/scratch/stefan/7769638/working/building/REAL300000057155 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057155

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057155/0 /scratch/stefan/7769638/working/building/REAL300000057155 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 162)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/162
`/scratch/stefan/7769638/working/3D/162' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN=C1Cl)

`REAL300000057155.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057155/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057155 none CN1C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 16, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 7, 7, 18, 19, 19, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 2, 2, 2, 7, 18, 54, 54, 54, 54, 54, 1] 54
rigid atoms, others: [0, 1, 2, 3, 32, 18, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057155 none CN1C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 16, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 34, 34, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 34, 10, 6, 1, 1, 1, 1, 54] 54
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057155 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057155
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057155/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057155
Building REAL300000057156
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057156'
/scratch/stefan/7769638/working/building/REAL300000057156 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057156

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057156/0 /scratch/stefan/7769638/working/building/REAL300000057156 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 163)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/163
`/scratch/stefan/7769638/working/3D/163' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3=CC=CC=C3)C=C2)C=C1)

`REAL300000057156.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057156.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057156/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057156 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3=CC=CC=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', 'N.am', '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.ar', 'C.ar', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 4, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 4, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1] 10
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 22
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057156 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3=CC=CC=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', 'N.am', '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.ar', 'C.ar', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 85, 85, 83, 85, 85, 80, 29, 28, 29, 11, 11, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 1, 1, 85, 85, 85, 85, 80, 28, 11, 1, 6, 6, 2, 6, 6, 1, 1, 85, 85] 85
rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 239
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057156 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3=CC=CC=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', 'N.am', '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.ar', 'C.ar', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 85, 85, 85, 85, 85, 84, 50, 50, 50, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 85, 85, 85, 85, 84, 50, 23, 6, 1, 1, 1, 1, 1, 6, 6, 85, 85] 85
rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40])
total number of confs: 223
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057156 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057156
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057156/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057156
Building REAL300000057157
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057157'
/scratch/stefan/7769638/working/building/REAL300000057157 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057157

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057157/0 /scratch/stefan/7769638/working/building/REAL300000057157 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 164)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/164
`/scratch/stefan/7769638/working/3D/164' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057157.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057157.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057157/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057157 none CCN1N=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 8, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 38, 44, 44, 38, 40, 44, 44, 44, 44, 6, 6, 6, 5, 5, 1, 4, 14, 38, 44, 44, 44, 44] 48
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 27] set([0, 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])
total number of confs: 173
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057157 none CCN1N=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 8, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 44, 44, 44, 44, 44, 34, 34, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 48, 48, 48, 48, 48, 44, 34, 14, 7, 1, 1, 1, 1] 48
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057157 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057157
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057157/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057157
Building REAL300000057158
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057158'
/scratch/stefan/7769638/working/building/REAL300000057158 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057158

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057158/0 /scratch/stefan/7769638/working/building/REAL300000057158 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 165)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/165
`/scratch/stefan/7769638/working/3D/165' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=C(F)C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057158.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057158.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057158/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057158 none NC1=C(F)C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', '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.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: [8, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 28, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 1, 1, 1, 11, 28, 49, 49, 49, 49, 49] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 139
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057158 none NC1=C(F)C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', '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.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: [8, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 31, 31, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 49, 49, 49, 49, 49, 31, 14, 7, 1, 1, 1, 1] 49
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 96
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057158 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057158
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057158/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057158
Building REAL300000057159
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057159'
/scratch/stefan/7769638/working/building/REAL300000057159 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000057159

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057159/0 /scratch/stefan/7769638/working/building/REAL300000057159 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 166)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/166
`/scratch/stefan/7769638/working/3D/166' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC[N@@H+]3CCCCC23)C=C1)

`REAL300000057159.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057159/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057159 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC[N@@H+]3CCCCC23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1] 14
rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 30
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057159 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC[N@@H+]3CCCCC23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 14
rigid atoms, others: [10, 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, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 44, 45, 23, 24, 25, 26, 27, 28])
total number of confs: 39
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057159 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057159/1 /scratch/stefan/7769638/working/building/REAL300000057159 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 167)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/167
`/scratch/stefan/7769638/working/3D/167' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC[N@H+]3CCCCC23)C=C1)

`REAL300000057159.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057159/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057159 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC[N@H+]3CCCCC23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 8, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1] 14
rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 33
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057159 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC[N@H+]3CCCCC23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 15
rigid atoms, others: [10, 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, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 44, 45, 23, 24, 25, 26, 27, 28])
total number of confs: 43
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057159 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `2'
/scratch/stefan/7769638/working/building/REAL300000057159/2 /scratch/stefan/7769638/working/building/REAL300000057159 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 2 (index: 168)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/168
`/scratch/stefan/7769638/working/3D/168' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3CCCCC23)C=C1)

`REAL300000057159.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000057159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057159/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057159 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3CCCCC23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 8, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 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, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 47
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057159 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3CCCCC23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 43, 44, 22, 23, 24, 25, 26, 27])
total number of confs: 47
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057159 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057159
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057159/0.*
2: /scratch/stefan/7769638/working/building/REAL300000057159/2.*
1: /scratch/stefan/7769638/working/building/REAL300000057159/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057159
Building REAL300000057160
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057160'
/scratch/stefan/7769638/working/building/REAL300000057160 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057160

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057160/0 /scratch/stefan/7769638/working/building/REAL300000057160 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 169)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/169
`/scratch/stefan/7769638/working/3D/169' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057160.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057160/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057160 none CC(C)C1CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
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, 26, 27, 27, 26, 26, 27, 27, 27, 27, 3, 3, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 26, 27, 27, 27, 27] 27
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 9, 10, 7, 11, 40, 35, 41, 36, 38, 37, 39, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45, 46, 47])
total number of confs: 88
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057160 none CC(C)C1CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 7, 1, 1, 1, 1] 27
rigid atoms, others: [44, 45, 14, 15, 16, 17, 18, 19, 46, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 60
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057160 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057160
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057160/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057160
Building REAL300000057161
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057161'
/scratch/stefan/7769638/working/building/REAL300000057161 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057161

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057161/0 /scratch/stefan/7769638/working/building/REAL300000057161 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 170)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/170
`/scratch/stefan/7769638/working/3D/170' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)C=C1)

`REAL300000057161.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057161.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057161/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057161 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 45, 45, 85, 85, 101, 101, 85, 85, 101, 101, 85, 101, 101, 85, 85, 1, 1, 1, 1, 10, 16, 45, 101, 101, 101, 101, 101, 101, 101, 85, 101, 101, 1, 1] 101
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 282
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057161 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [103, 103, 103, 103, 103, 103, 97, 52, 52, 52, 23, 23, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 103, 103, 103, 103, 97, 52, 23, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 103, 103] 103
rigid atoms, others: [39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45])
total number of confs: 280
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057161 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [87, 86, 87, 86, 87, 87, 82, 37, 37, 37, 13, 13, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 1, 5, 5, 1, 1, 87, 87, 87, 87, 82, 37, 13, 3, 3, 3, 3, 3, 5, 5, 1, 5, 5, 87, 87] 103
rigid atoms, others: [12, 13, 14, 15, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 259
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057161 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [103, 103, 103, 103, 103, 103, 97, 48, 48, 48, 20, 20, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 3, 3, 103, 103, 103, 103, 97, 48, 20, 1, 1, 1, 1, 1, 5, 5, 3, 5, 5, 103, 103] 103
rigid atoms, others: [34, 35, 36, 37, 38, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 282
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057161 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057161
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057161/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057161
Building REAL300000057162
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057162'
/scratch/stefan/7769638/working/building/REAL300000057162 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057162

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057162/0 /scratch/stefan/7769638/working/building/REAL300000057162 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 171)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/171
`/scratch/stefan/7769638/working/3D/171' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=CN=C1C)

`REAL300000057162.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057162.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057162/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057162 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=CN=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 51, 51, 43, 51, 51, 51, 26, 26, 26, 14, 7, 1, 1, 1, 1, 51, 51, 51, 51, 51] 51
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36])
total number of confs: 141
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057162 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=CN=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 31, 31, 31, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 31, 51, 51, 51, 51, 51, 1, 1, 2, 2, 2] 51
rigid atoms, others: [32, 1, 33, 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, 34, 35, 36])
total number of confs: 145
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057162 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057162
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057162/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057162
Building REAL300000057163
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057163'
/scratch/stefan/7769638/working/building/REAL300000057163 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057163

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057163/0 /scratch/stefan/7769638/working/building/REAL300000057163 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 172)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/172
`/scratch/stefan/7769638/working/3D/172' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC=C1C1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057163.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057163.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057163/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057163 none CN1N=CC=C1C1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 1, 7, 7, 7, 7, 7, 19, 19, 19, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 19, 36, 36, 36, 36, 36, 7, 7] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057163 none CN1N=CC=C1C1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 24, 25, 25, 24, 24, 25, 25, 25, 25, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 24, 25, 25, 25, 25, 1, 1] 36
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 41, 24, 42, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057163 none CN1N=CC=C1C1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 25, 25, 25, 25, 25, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 36, 36, 36, 36, 36, 25, 25, 25, 25, 25, 15, 7, 1, 1, 1, 1, 25, 25] 36
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 72
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057163 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057163
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057163/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057163
Building REAL300000057164
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057164'
/scratch/stefan/7769638/working/building/REAL300000057164 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057164

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057164/0 /scratch/stefan/7769638/working/building/REAL300000057164 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 173)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/173
`/scratch/stefan/7769638/working/3D/173' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)[O-])=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057164.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057164.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057164/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057164 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 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, 3, 3, 1, 1, 4, 4, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 4, 6, 9, 9, 9, 9, 9] 9
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])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057164 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 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, 6, 6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 6, 5, 1, 1, 1, 1] 9
rigid atoms, others: [32, 33, 34, 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: 20
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057164 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057164
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057164/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057164
Building REAL300000057165
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057165'
/scratch/stefan/7769638/working/building/REAL300000057165 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057165

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057165/0 /scratch/stefan/7769638/working/building/REAL300000057165 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 174)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/174
`/scratch/stefan/7769638/working/3D/174' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(N2C=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=C2)C=N1)

`REAL300000057165.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057165.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057165/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057165 none CN1C=C(N2C=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 5, 5, 5, 5, 17, 17, 41, 41, 41, 114, 117, 117, 114, 117, 117, 117, 117, 117, 5, 1, 1, 2, 2, 2, 1, 5, 5, 17, 41, 114, 117, 117, 117, 117, 5, 1] 117
rigid atoms, others: [0, 1, 2, 3, 4, 40, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057165 none CN1C=C(N2C=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 72, 81, 81, 72, 77, 81, 81, 81, 81, 1, 5, 5, 5, 5, 5, 5, 1, 1, 9, 25, 72, 81, 81, 81, 81, 1, 5] 117
rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 23, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 40])
total number of confs: 257
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057165 none CN1C=C(N2C=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 81, 81, 81, 81, 52, 52, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 81, 117, 117, 117, 117, 117, 117, 81, 81, 52, 16, 7, 1, 1, 1, 1, 81, 117] 117
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40])
total number of confs: 220
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057165 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057165
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057165/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057165
Building REAL300000057166
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057166'
/scratch/stefan/7769638/working/building/REAL300000057166 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057166

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057166/0 /scratch/stefan/7769638/working/building/REAL300000057166 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 175)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/175
`/scratch/stefan/7769638/working/3D/175' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C2C(=C1)CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057166.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057166.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057166/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057166 none CC1=CC(C)=C2C(=C1)CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 5, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 35, 32, 36, 33, 28] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 37, 38, 39, 40, 41, 42])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057166 none CC1=CC(C)=C2C(=C1)CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 7, 1, 1, 1, 1] 18
rigid atoms, others: [39, 40, 41, 42, 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, 36, 37, 38])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057166 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057166
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057166/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057166
Building REAL300000057167
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057167'
/scratch/stefan/7769638/working/building/REAL300000057167 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057167

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057167/0 /scratch/stefan/7769638/working/building/REAL300000057167 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 176)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/176
`/scratch/stefan/7769638/working/3D/176' -> `0.mol2'
Preparing input files

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

`REAL300000057167.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057167.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057167/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057167 none CC(C)(C#N)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 23, 24, 24, 51, 53, 53, 52, 53, 53, 53, 53, 53, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 7, 23, 51, 53, 53, 53, 53, 1, 1] 109
rigid atoms, others: [32, 1, 5, 6, 7, 8, 9, 42, 41, 24, 25, 33] set([0, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057167 none CC(C)(C#N)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 49, 109, 109, 109, 30, 53, 53, 30, 30, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 109, 109, 109, 109, 109, 109, 53, 53, 30, 12, 7, 1, 1, 1, 1, 53, 53] 109
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 474
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057167 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057167
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057167/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057167
Building REAL300000057168
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057168'
/scratch/stefan/7769638/working/building/REAL300000057168 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057168

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057168/0 /scratch/stefan/7769638/working/building/REAL300000057168 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 177)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/177
`/scratch/stefan/7769638/working/3D/177' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CS1)

`REAL300000057168.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057168.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057168/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057168 none CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 30, 30, 30, 30, 30, 1, 1] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 36, 19, 20, 24, 25, 26, 27, 28, 35] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 29, 30, 31])
total number of confs: 75
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057168 none CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 7, 1, 1, 1, 1, 30, 30] 30
rigid atoms, others: [32, 33, 34, 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, 35, 36])
total number of confs: 61
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057168 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057168
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057168/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057168
Building REAL300000057169
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057169'
/scratch/stefan/7769638/working/building/REAL300000057169 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057169

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057169/0 /scratch/stefan/7769638/working/building/REAL300000057169 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 178)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/178
`/scratch/stefan/7769638/working/3D/178' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3C=CN=C23)C=C1)

`REAL300000057169.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057169.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057169/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057169 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3C=CN=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 8, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 8, 18, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057169 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3C=CN=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 18, 19, 19, 18, 5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 22, 23, 24, 25, 26, 36])
total number of confs: 52
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057169 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057169
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057169/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057169
Building REAL300000057170
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057170'
/scratch/stefan/7769638/working/building/REAL300000057170 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057170

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057170/0 /scratch/stefan/7769638/working/building/REAL300000057170 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 179)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/179
`/scratch/stefan/7769638/working/3D/179' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)O1)

`REAL300000057170.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057170/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057170 none COC(=O)C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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: [11, 11, 1, 11, 1, 1, 1, 1, 8, 8, 29, 29, 29, 61, 65, 65, 63, 65, 65, 65, 65, 65, 1, 1, 1, 11, 11, 11, 1, 8, 28, 61, 65, 65, 65, 65, 2, 2, 2] 86
rigid atoms, others: [2, 4, 5, 6, 7, 22, 23, 24, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057170 none COC(=O)C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [86, 86, 65, 86, 65, 65, 34, 34, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 65, 65, 65, 86, 86, 86, 65, 34, 12, 7, 1, 1, 1, 1, 65, 65, 65] 86
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057170 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057170
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057170/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057170
Building REAL300000057171
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057171'
/scratch/stefan/7769638/working/building/REAL300000057171 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057171

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057171/0 /scratch/stefan/7769638/working/building/REAL300000057171 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 180)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/180
`/scratch/stefan/7769638/working/3D/180' -> `0.mol2'
Preparing input files

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

`REAL300000057171.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057171.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057171/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057171 none CC(C)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 1, 10, 10, 25, 25, 25, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 25, 43, 43, 43, 43, 43] 43
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 33, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 119
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057171 none CC(C)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 24, 43, 43, 24, 24, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 24, 43, 43, 24, 14, 7, 1, 1, 1, 1] 43
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 120
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057171 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057171
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057171/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057171
Building REAL300000057172
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057172'
/scratch/stefan/7769638/working/building/REAL300000057172 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057172

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057172/0 /scratch/stefan/7769638/working/building/REAL300000057172 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 181)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/181
`/scratch/stefan/7769638/working/3D/181' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(O)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057172.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057172.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057172/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057172 none COC1=CC(O)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 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
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 59, 63, 63, 61, 61, 63, 63, 63, 63, 1, 3, 3, 3, 1, 2, 1, 11, 33, 59, 63, 63, 63, 63, 1] 128
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 23, 27, 29, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 193
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057172 none COC1=CC(O)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 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
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [64, 63, 63, 42, 63, 63, 63, 25, 25, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 64, 64, 64, 42, 126, 63, 25, 10, 6, 1, 1, 1, 1, 63] 128
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])
total number of confs: 283
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057172 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057172
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057172/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057172
Building REAL300000057173
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057173'
/scratch/stefan/7769638/working/building/REAL300000057173 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057173

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057173/0 /scratch/stefan/7769638/working/building/REAL300000057173 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 182)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/182
`/scratch/stefan/7769638/working/3D/182' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057173.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057173.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057173/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057173 none N#CC1=CC=C2C(=C1)NC(=O)C2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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, 5, 6, 6, 17, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 5, 17, 18, 18, 18, 18] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057173 none N#CC1=CC=C2C(=C1)NC(=O)C2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 16, 7, 1, 1, 1, 1] 18
rigid atoms, others: [32, 33, 34, 35, 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])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057173 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057173
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057173/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057173
Building REAL300000057174
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057174'
/scratch/stefan/7769638/working/building/REAL300000057174 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057174

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057174/0 /scratch/stefan/7769638/working/building/REAL300000057174 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 183)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/183
`/scratch/stefan/7769638/working/3D/183' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN3CCCCC3=C2)C=C1)

`REAL300000057174.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057174.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057174/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057174 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN3CCCCC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 4, 6, 6, 6, 22, 22, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 6, 22, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 52
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057174 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN3CCCCC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 10, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 29
rigid atoms, others: [32, 33, 34, 35, 36, 37, 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, 38, 22, 23, 24, 25, 26, 27, 28, 39])
total number of confs: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057174 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057174
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057174/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057174
Building REAL300000057175
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057175'
/scratch/stefan/7769638/working/building/REAL300000057175 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057175

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057175/0 /scratch/stefan/7769638/working/building/REAL300000057175 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 184)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/184
`/scratch/stefan/7769638/working/3D/184' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=CNC1=O)

`REAL300000057175.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057175.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057175/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057175 none N#CC1=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=CNC1=O NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 9, 9, 9, 17, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 17, 18, 18, 18, 18, 1, 1] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40] set([33, 34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21])
total number of confs: 43
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057175 none N#CC1=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=CNC1=O NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 7, 1, 1, 1, 1, 18, 18] 18
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 47
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057175 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057175/1 /scratch/stefan/7769638/working/building/REAL300000057175 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 185)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/185
`/scratch/stefan/7769638/working/3D/185' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C[N-]C1=O)

`REAL300000057175.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057175.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057175/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057175 none N#CC1=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C[N-]C1=O NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 9, 9, 9, 21, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 22, 22, 22, 22, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39] set([33, 34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21])
total number of confs: 55
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057175 none N#CC1=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C[N-]C1=O NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 7, 1, 1, 1, 1, 22] 22
rigid atoms, others: [35, 36, 37, 38, 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, 39])
total number of confs: 50
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057175 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057175
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057175/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057175/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057175
Building REAL300000057176
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057176'
/scratch/stefan/7769638/working/building/REAL300000057176 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057176

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057176/0 /scratch/stefan/7769638/working/building/REAL300000057176 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 186)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/186
`/scratch/stefan/7769638/working/3D/186' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CC3(F)F)CC2)C=C1)

`REAL300000057176.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057176.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057176/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057176 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CC3(F)F)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 7, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 32
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 58
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057176 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CC3(F)F)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 32
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 22, 23, 24, 25, 26, 27])
total number of confs: 81
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057176 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057176
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057176/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057176
Building REAL300000057177
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057177'
/scratch/stefan/7769638/working/building/REAL300000057177 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057177

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057177/0 /scratch/stefan/7769638/working/building/REAL300000057177 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 187)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/187
`/scratch/stefan/7769638/working/3D/187' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=C1)C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(=O)N2C)

`REAL300000057177.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057177.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057177/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057177 none COC1=CC=C2C(=C1)C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(=O)N2C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 7, 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, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 32, 38, 38, 32, 34, 38, 38, 38, 38, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 32, 38, 38, 38, 38, 1, 1, 1] 38
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 40, 41, 23, 24, 25, 26, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057177 none COC1=CC=C2C(=C1)C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(=O)N2C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 7, 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, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 19, 19, 7, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 19, 7, 1, 1, 1, 1, 38, 38, 38] 38
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40, 41])
total number of confs: 81
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057177 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057177
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057177/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057177
Building REAL300000057178
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057178'
/scratch/stefan/7769638/working/building/REAL300000057178 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057178

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057178/0 /scratch/stefan/7769638/working/building/REAL300000057178 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 188)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/188
`/scratch/stefan/7769638/working/3D/188' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C(C)(C)CCCC(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057178.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057178/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057178 none CCOC(=O)C(C)(C)CCCC(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 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, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [184, 166, 162, 95, 162, 63, 95, 95, 61, 58, 27, 27, 27, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 95, 95, 95, 95, 95, 95, 63, 63, 63, 63, 58, 58, 27, 27, 27, 9, 5, 1, 1, 1, 1] 184
rigid atoms, others: [51, 49, 50, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 754
number of broken/clashed sets: 142
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057178 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057178
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057178/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057178
Building REAL300000057179
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057179'
/scratch/stefan/7769638/working/building/REAL300000057179 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057179

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057179/0 /scratch/stefan/7769638/working/building/REAL300000057179 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 189)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/189
`/scratch/stefan/7769638/working/3D/189' -> `0.mol2'
Preparing input files

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

`REAL300000057179.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057179.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057179/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057179 none CC(C)CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [50, 49, 50, 35, 35, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 48, 48, 35, 41, 48, 48, 50, 50, 50, 50, 50, 50, 50, 49, 49, 14, 7, 1, 1, 1, 1, 48, 48, 48, 48] 52
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44])
total number of confs: 214
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057179 none CC(C)CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [15, 14, 15, 7, 1, 7, 7, 22, 22, 22, 43, 48, 48, 45, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 14, 14, 22, 43, 48, 48, 48, 48, 1, 1, 1, 1] 52
rigid atoms, others: [4, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 181
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057179 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057179
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057179/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057179
Building REAL300000057180
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057180'
/scratch/stefan/7769638/working/building/REAL300000057180 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000057180

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057180/0 /scratch/stefan/7769638/working/building/REAL300000057180 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 190)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/190
`/scratch/stefan/7769638/working/3D/190' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1CC1=CC=CC=C1)

`REAL300000057180.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057180/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057180 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 31, 38, 38, 31, 31, 38, 38, 38, 38, 1, 1, 1, 3, 5, 5, 3, 5, 5, 2, 2, 2, 2, 2, 2, 1, 1, 8, 31, 38, 38, 38, 38, 1, 1, 3, 3, 5, 5, 5, 5, 5] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 42, 43, 34, 35, 20, 21, 6] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 167
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057180 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [38, 38, 38, 38, 38, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 49, 49, 49, 49, 49, 49, 38, 38, 38, 38, 38, 38, 38, 38, 13, 7, 1, 1, 1, 1, 38, 38, 49, 49, 49, 49, 49, 49, 49] 49
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 132
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057180 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 25, 49, 49, 49, 49, 49, 5, 5, 2, 2, 1, 1, 1, 1, 1] 49
rigid atoms, others: [46, 47, 48, 49, 50, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 134
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057180 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057180/1 /scratch/stefan/7769638/working/building/REAL300000057180 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 191)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/191
`/scratch/stefan/7769638/working/3D/191' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=C1)

`REAL300000057180.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057180/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057180 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 8, 8, 30, 41, 41, 36, 40, 41, 41, 41, 41, 1, 1, 1, 1, 3, 4, 4, 3, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1, 7, 30, 41, 41, 41, 41, 1, 1, 3, 3, 4, 4, 4, 4, 4] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 43, 44, 35, 20, 21, 22, 36, 6] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 151
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057180 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 19, 19, 7, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 42, 42, 42, 42, 42, 42, 41, 41, 41, 41, 41, 41, 41, 41, 19, 7, 1, 1, 1, 1, 41, 41, 42, 42, 42, 42, 42, 42, 42] 42
rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 85
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057180 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 37, 42, 42, 40, 42, 42, 42, 42, 42, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 15, 37, 42, 42, 42, 42, 4, 4, 2, 2, 1, 1, 1, 1, 1] 42
rigid atoms, others: [47, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 119
number of broken/clashed sets: 42
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057180 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `2'
/scratch/stefan/7769638/working/building/REAL300000057180/2 /scratch/stefan/7769638/working/building/REAL300000057180 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 2 (index: 192)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/192
`/scratch/stefan/7769638/working/3D/192' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=C1)

`REAL300000057180.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000057180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057180/2/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', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057180 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 8, 8, 30, 40, 40, 30, 30, 40, 40, 40, 40, 1, 1, 1, 1, 3, 4, 4, 3, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1, 7, 30, 40, 40, 40, 40, 1, 1, 3, 3, 4, 4, 3, 4, 4] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 43, 44, 35, 20, 21, 22, 36, 6] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 188
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057180 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [40, 40, 40, 40, 40, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 40, 41, 41, 41, 41, 41, 41, 40, 40, 40, 40, 40, 40, 40, 40, 18, 7, 1, 1, 1, 1, 40, 40, 41, 41, 41, 41, 41, 41, 41] 41
rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 87
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057180 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 36, 41, 41, 36, 36, 41, 41, 41, 41, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 15, 36, 41, 41, 41, 41, 4, 4, 2, 2, 1, 1, 1, 1, 1] 41
rigid atoms, others: [47, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 142
number of broken/clashed sets: 41
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057180 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057180
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057180/0.*
2: /scratch/stefan/7769638/working/building/REAL300000057180/2.*
1: /scratch/stefan/7769638/working/building/REAL300000057180/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057180
Building REAL300000057181
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057181'
/scratch/stefan/7769638/working/building/REAL300000057181 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057181

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057181/0 /scratch/stefan/7769638/working/building/REAL300000057181 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 193)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/193
`/scratch/stefan/7769638/working/3D/193' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C)CCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057181.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057181.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057181/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057181 none CCC1(C)CCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 20, 23, 23, 20, 20, 23, 23, 23, 23, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 20, 23, 23, 23, 23] 26
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 33, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41])
total number of confs: 98
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057181 none CCC1(C)CCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 23, 23, 23, 23, 23, 23, 23, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 26, 26, 26, 26, 23, 23, 23, 23, 23, 23, 23, 23, 23, 15, 7, 1, 1, 1, 1] 26
rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 76
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057181 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057181
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057181/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057181
Building REAL300000057182
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057182'
/scratch/stefan/7769638/working/building/REAL300000057182 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057182

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057182/0 /scratch/stefan/7769638/working/building/REAL300000057182 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 194)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/194
`/scratch/stefan/7769638/working/3D/194' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC1=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CS1)

`REAL300000057182.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057182.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057182/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057182 none CN(C)CC1=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [23, 8, 23, 1, 1, 1, 1, 1, 8, 8, 29, 30, 30, 76, 103, 103, 76, 83, 103, 103, 103, 103, 1, 1, 23, 23, 23, 23, 23, 23, 8, 8, 8, 29, 76, 103, 103, 103, 103, 1] 192
rigid atoms, others: [3, 4, 5, 6, 7, 39, 22, 23] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 490
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057182 none CN(C)CC1=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [192, 190, 192, 103, 103, 103, 53, 53, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 103, 103, 192, 192, 192, 192, 192, 192, 190, 190, 53, 18, 7, 1, 1, 1, 1, 103] 192
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 616
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057182 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057182
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057182/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057182
Building REAL300000057183
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057183'
/scratch/stefan/7769638/working/building/REAL300000057183 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057183

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057183/0 /scratch/stefan/7769638/working/building/REAL300000057183 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 195)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/195
`/scratch/stefan/7769638/working/3D/195' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC2=C1OC(C)(C)CC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057183.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057183.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057183/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057183 none COC1=CC=CC2=C1OC(C)(C)CC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.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', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 9, 9, 9, 35, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 9, 35, 39, 39, 39, 39] 39
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 33, 31] set([0, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47])
total number of confs: 110
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057183 none COC1=CC=CC2=C1OC(C)(C)CC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.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', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 7, 1, 1, 1, 1] 39
rigid atoms, others: [44, 45, 46, 47, 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, 40, 41, 42, 43])
total number of confs: 73
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057183 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057183
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057183/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057183
Building REAL300000057184
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057184'
/scratch/stefan/7769638/working/building/REAL300000057184 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057184

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057184/0 /scratch/stefan/7769638/working/building/REAL300000057184 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 196)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/196
`/scratch/stefan/7769638/working/3D/196' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057184.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057184.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057184/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057184 none NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 21, 22, 22, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 5, 5, 1, 1, 8, 21, 42, 42, 42, 42, 42] 124
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 134
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057184 none NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [124, 42, 124, 124, 42, 42, 42, 29, 29, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 124, 124, 42, 42, 29, 10, 6, 1, 1, 1, 1] 124
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: 413
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057184 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057184
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057184/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057184
Building REAL300000057185
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057185'
/scratch/stefan/7769638/working/building/REAL300000057185 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057185

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057185/0 /scratch/stefan/7769638/working/building/REAL300000057185 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 197)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/197
`/scratch/stefan/7769638/working/3D/197' -> `0.mol2'
Preparing input files

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

`REAL300000057185.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057185.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057185/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057185 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 3, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 3, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8] 8
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 25
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057185 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 3, 3, 3, 3, 8, 8, 8, 8, 8, 1, 1, 3, 3, 1, 3, 3, 1] 8
rigid atoms, others: [1, 37, 38, 44, 16, 17, 18, 19, 20, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43])
total number of confs: 28
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057185 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [4, 3, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 3] 8
rigid atoms, others: [39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44])
total number of confs: 20
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057185 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057185
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057185/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057185
Building REAL300000057186
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057186'
/scratch/stefan/7769638/working/building/REAL300000057186 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057186

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057186/0 /scratch/stefan/7769638/working/building/REAL300000057186 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 198)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/198
`/scratch/stefan/7769638/working/3D/198' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057186.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057186.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057186/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057186 none CC1CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33, 35, 32, 25, 26, 27, 28, 29, 30, 31] set([36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 47
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057186 none CC1CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 7, 1, 1, 1, 1] 16
rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 43
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057186 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057186
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057186/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057186
Building REAL300000057187
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057187'
/scratch/stefan/7769638/working/building/REAL300000057187 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057187

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057187/0 /scratch/stefan/7769638/working/building/REAL300000057187 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 199)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/199
`/scratch/stefan/7769638/working/3D/199' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=NN2C2=CC=CC=C2)C=C1)

`REAL300000057187.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057187/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057187 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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, 1, 1, 1, 5, 9, 9, 9, 21, 21, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 5, 9, 21, 36, 36, 36, 36, 36, 36, 1, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 37] set([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: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057187 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [94, 91, 94, 90, 94, 94, 90, 47, 46, 47, 12, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 94, 94, 94, 94, 90, 46, 12, 1, 5, 5, 3, 5, 5, 94, 94] 98
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057187 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 96, 98, 96, 98, 98, 96, 55, 55, 55, 21, 21, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 96, 55, 21, 5, 1, 1, 1, 1, 1, 98, 98] 98
rigid atoms, others: [32, 33, 34, 35, 36, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38])
total number of confs: 284
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057187 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057187
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057187/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057187
Building REAL300000057188
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057188'
/scratch/stefan/7769638/working/building/REAL300000057188 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057188

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057188/0 /scratch/stefan/7769638/working/building/REAL300000057188 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 200)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/200
`/scratch/stefan/7769638/working/3D/200' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CN=CC=C3O2)C=C1)

`REAL300000057188.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057188.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057188/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057188 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CN=CC=C3O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 8, 8, 8, 25, 25, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 6, 8, 25, 34, 34, 34, 34, 1, 1] 34
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: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057188 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CN=CC=C3O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 15, 7, 1, 1, 1, 1, 34, 34] 34
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, 34, 33, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057188 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057188
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057188/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057188
Building REAL300000057189
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057189'
/scratch/stefan/7769638/working/building/REAL300000057189 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057189

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057189/0 /scratch/stefan/7769638/working/building/REAL300000057189 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 201)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/201
`/scratch/stefan/7769638/working/3D/201' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(OC)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F)

`REAL300000057189.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057189.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057189/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057189 none COC1=CC(OC)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 1, 1, 6, 6, 22, 22, 22, 60, 68, 68, 64, 66, 68, 68, 68, 68, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 22, 60, 68, 68, 68, 68, 1] 89
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 40, 23, 24, 25, 29] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057189 none COC1=CC(OC)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [89, 39, 39, 68, 68, 68, 89, 39, 39, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 68, 68, 68, 89, 89, 89, 68, 89, 89, 89, 39, 15, 7, 1, 1, 1, 1, 68] 89
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])
total number of confs: 296
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057189 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057189
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057189/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057189
Building REAL300000057190
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057190'
/scratch/stefan/7769638/working/building/REAL300000057190 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057190

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057190/0 /scratch/stefan/7769638/working/building/REAL300000057190 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 202)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/202
`/scratch/stefan/7769638/working/3D/202' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=C(F)C(Cl)=C32)C=C1)

`REAL300000057190.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057190/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057190 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=C(F)C(Cl)=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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, 10, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 10, 13, 17, 17, 17, 17, 17, 17, 1, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 23, 24, 25, 26, 36] set([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: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057190 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=C(F)C(Cl)=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 17, 17] 17
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 23, 24, 25, 26, 27, 28, 36])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057190 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057190
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057190/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057190
Building REAL300000057191
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057191'
/scratch/stefan/7769638/working/building/REAL300000057191 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057191

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057191/0 /scratch/stefan/7769638/working/building/REAL300000057191 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 203)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/203
`/scratch/stefan/7769638/working/3D/203' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC)

`REAL300000057191.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057191/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057191 none COC1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 27, 28, 28, 64, 79, 79, 69, 79, 79, 79, 79, 79, 1, 1, 1, 3, 4, 4, 4, 1, 10, 27, 64, 79, 79, 79, 79, 1, 3, 3, 3] 100
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 29, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057191 none COC1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 79, 79, 79, 79, 79, 42, 42, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 79, 79, 79, 100, 100, 100, 100, 79, 42, 18, 7, 1, 1, 1, 1, 79, 100, 100, 100] 100
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057191 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057191
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057191/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057191
Building REAL300000057192
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057192'
/scratch/stefan/7769638/working/building/REAL300000057192 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057192

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057192/0 /scratch/stefan/7769638/working/building/REAL300000057192 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 204)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/204
`/scratch/stefan/7769638/working/3D/204' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1)

`REAL300000057192.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057192.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057192/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057192 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 8, 8, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 2, 2, 2, 1, 1, 8, 15, 32, 32, 32, 32, 32, 1] 32
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: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057192 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 27, 27, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 27, 12, 7, 1, 1, 1, 1, 32] 32
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 67
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057192 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057192
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057192/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057192
Building REAL300000057193
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057193'
/scratch/stefan/7769638/working/building/REAL300000057193 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057193

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057193/0 /scratch/stefan/7769638/working/building/REAL300000057193 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 205)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/205
`/scratch/stefan/7769638/working/3D/205' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057193.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057193.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057193/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057193 none CCC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 55, 59, 59, 56, 59, 59, 59, 59, 59, 1, 3, 3, 3, 2, 2, 1, 1, 1, 9, 29, 55, 59, 59, 59, 59, 1] 101
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22, 38, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057193 none CCC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 59, 59, 50, 59, 59, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 101, 101, 101, 101, 101, 49, 59, 59, 34, 16, 7, 1, 1, 1, 1, 59] 101
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, 38])
total number of confs: 376
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057193 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057193
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057193/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057193
Building REAL300000057194
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057194'
/scratch/stefan/7769638/working/building/REAL300000057194 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057194

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057194/0 /scratch/stefan/7769638/working/building/REAL300000057194 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 206)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/206
`/scratch/stefan/7769638/working/3D/206' -> `0.mol2'
Preparing input files

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

`REAL300000057194.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057194.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057194/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057194 none CC(C)CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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, 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: [46, 45, 46, 30, 30, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 42, 42, 30, 42, 42, 46, 46, 46, 46, 46, 46, 46, 45, 45, 11, 7, 1, 1, 1, 1, 42, 42, 42, 42] 47
rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43])
total number of confs: 186
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057194 none CC(C)CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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, 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, 13, 14, 7, 1, 7, 7, 19, 19, 19, 37, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 13, 13, 19, 37, 42, 42, 42, 42, 1, 1, 1, 1] 47
rigid atoms, others: [4, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 151
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057194 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057194
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057194/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057194
Building REAL300000057195
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057195'
/scratch/stefan/7769638/working/building/REAL300000057195 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057195

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057195/0 /scratch/stefan/7769638/working/building/REAL300000057195 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 207)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/207
`/scratch/stefan/7769638/working/3D/207' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1)

`REAL300000057195.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057195/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057195 none NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 11, 11, 17, 17, 17, 37, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 5, 5, 1, 1, 11, 17, 37, 39, 39, 39, 39, 1] 91
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 24, 25, 28, 29, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057195 none NS(=O)(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 39, 91, 91, 31, 39, 39, 26, 26, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 91, 91, 39, 39, 26, 10, 7, 1, 1, 1, 1, 39] 91
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])
total number of confs: 354
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057195 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057195
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057195/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057195
Building REAL300000057196
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057196'
/scratch/stefan/7769638/working/building/REAL300000057196 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057196

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057196/0 /scratch/stefan/7769638/working/building/REAL300000057196 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 208)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/208
`/scratch/stefan/7769638/working/3D/208' -> `0.mol2'
Preparing input files

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

`REAL300000057196.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057196/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057196 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(O)C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'Br', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 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]
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: [28, 28, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 69, 69, 69, 69, 69, 69, 69, 28, 28, 28, 16, 7, 1, 1, 1, 1, 69, 69, 138, 69] 138
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 255
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057196 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(O)C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'Br', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 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]
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: [11, 1, 11, 11, 36, 36, 36, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 36, 69, 69, 69, 69, 69, 1, 1, 2, 1] 138
rigid atoms, others: [1, 34, 36, 33, 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, 35])
total number of confs: 195
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057196 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057196/1 /scratch/stefan/7769638/working/building/REAL300000057196 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 209)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/209
`/scratch/stefan/7769638/working/3D/209' -> `1.mol2'
Preparing input files

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

`REAL300000057196.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057196/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057196 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C([O-])C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'Br', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 17, 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, 2, 2, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 83, 83, 83, 83, 83, 83, 83, 28, 28, 28, 18, 7, 1, 1, 1, 1, 83, 83, 83] 83
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 137
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057196 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C([O-])C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'Br', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 17, 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, 2, 2, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 41, 41, 41, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 41, 83, 83, 83, 83, 83, 1, 1, 1] 83
rigid atoms, others: [1, 34, 35, 33, 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])
total number of confs: 223
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057196 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057196
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057196/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057196/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057196
Building REAL300000057197
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057197'
/scratch/stefan/7769638/working/building/REAL300000057197 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057197

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057197/0 /scratch/stefan/7769638/working/building/REAL300000057197 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 210)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/210
`/scratch/stefan/7769638/working/3D/210' -> `0.mol2'
Preparing input files

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

`REAL300000057197.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057197.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057197/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057197 none COCC(CC(C)(C)C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 5, 5, 5, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [106, 100, 38, 38, 38, 48, 66, 66, 66, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 100, 100, 48, 48, 66, 66, 66, 66, 66, 66, 66, 66, 66, 16, 7, 1, 1, 1, 1] 116
rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 518
number of broken/clashed sets: 109
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057197 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057197
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057197/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057197
Building REAL300000057198
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057198'
/scratch/stefan/7769638/working/building/REAL300000057198 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057198

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057198/0 /scratch/stefan/7769638/working/building/REAL300000057198 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 211)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/211
`/scratch/stefan/7769638/working/3D/211' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(O)C=C2F)C=C1)

`REAL300000057198.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057198.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057198/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057198 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(O)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 4, 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, 1, 1, 10, 10, 10, 10, 24, 24, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 10, 10, 24, 28, 28, 56, 28, 1, 1] 56
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057198 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(O)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 13, 12, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 12, 8, 1, 1, 2, 1, 27, 27] 54
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 30, 32, 33])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057198 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057198
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057198/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057198
Building REAL300000057199
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057199'
/scratch/stefan/7769638/working/building/REAL300000057199 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057199

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057199/0 /scratch/stefan/7769638/working/building/REAL300000057199 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 212)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/212
`/scratch/stefan/7769638/working/3D/212' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(CC)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057199.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057199.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057199/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057199 none CCC1(CC)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 3, 1, 1, 1, 1, 1, 9, 9, 9, 51, 65, 65, 51, 51, 65, 65, 65, 65, 1, 1, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 1, 1, 1, 1, 9, 51, 65, 65, 65, 65, 1, 1, 1, 1] 91
rigid atoms, others: [1, 2, 3, 36, 5, 6, 7, 8, 9, 44, 34, 46, 45, 35, 22, 23, 47, 37] set([0, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43])
total number of confs: 251
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057199 none CCC1(CC)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [91, 65, 65, 65, 91, 65, 65, 65, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 65, 65, 65, 65, 18, 7, 1, 1, 1, 1, 65, 65, 65, 65] 91
rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47])
total number of confs: 421
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057199 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057199
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057199/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057199
Building REAL300000057200
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057200'
/scratch/stefan/7769638/working/building/REAL300000057200 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057200

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057200/0 /scratch/stefan/7769638/working/building/REAL300000057200 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 213)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/213
`/scratch/stefan/7769638/working/3D/213' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057200.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057200.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057200/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057200 none C=CCC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [18, 7, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 31, 37, 37, 31, 33, 37, 37, 37, 37, 1, 18, 18, 18, 7, 7, 1, 1, 1, 1, 1, 7, 31, 37, 37, 37, 37, 1, 1] 67
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 38, 39, 21, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37])
total number of confs: 179
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057200 none C=CCC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 37, 37, 37, 37, 37, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 67, 67, 67, 67, 67, 37, 37, 37, 37, 37, 16, 7, 1, 1, 1, 1, 37, 37] 67
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 232
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057200 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057200
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057200/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057200
Building REAL300000057201
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057201'
/scratch/stefan/7769638/working/building/REAL300000057201 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057201

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057201/0 /scratch/stefan/7769638/working/building/REAL300000057201 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 214)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/214
`/scratch/stefan/7769638/working/3D/214' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC(C)=CC=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057201.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057201/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057201 none CC1=NN(C2=CC(C)=CC=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 2, 7, 7, 1, 1, 1, 11, 11, 39, 39, 39, 94, 101, 101, 98, 101, 101, 101, 101, 101, 2, 2, 2, 7, 7, 7, 7, 5, 7, 7, 1, 11, 39, 94, 101, 101, 101, 101] 153
rigid atoms, others: [0, 1, 2, 3, 4, 38, 11, 12, 13] set([5, 6, 7, 8, 9, 10, 14, 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])
total number of confs: 299
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057201 none CC1=NN(C2=CC(C)=CC=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 33, 79, 79, 79, 149, 153, 153, 153, 153, 153, 153, 153, 153, 7, 7, 7, 1, 2, 2, 2, 1, 1, 1, 7, 33, 79, 149, 153, 153, 153, 153] 153
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 35, 36, 37, 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, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 418
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057201 none CC1=NN(C2=CC(C)=CC=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 101, 101, 101, 153, 153, 153, 153, 153, 153, 101, 51, 51, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 153, 153, 153, 153, 153, 153, 153, 101, 51, 18, 7, 1, 1, 1, 1] 153
rigid atoms, others: [42, 43, 44, 45, 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, 40, 41])
total number of confs: 269
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057201 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057201
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057201/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057201
Building REAL300000057202
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057202'
/scratch/stefan/7769638/working/building/REAL300000057202 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057202

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057202/0 /scratch/stefan/7769638/working/building/REAL300000057202 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 215)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/215
`/scratch/stefan/7769638/working/3D/215' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1)

`REAL300000057202.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057202.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057202/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057202 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 2, 2, 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: [2, 1, 1, 1, 1, 1, 1, 11, 11, 23, 23, 23, 54, 57, 57, 54, 54, 57, 57, 57, 57, 1, 1, 1, 3, 3, 3, 1, 1, 11, 23, 54, 57, 57, 57, 57, 1] 57
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 36, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 181
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057202 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 38, 57, 57, 35, 35, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 35, 14, 7, 1, 1, 1, 1, 57] 57
rigid atoms, others: [32, 33, 34, 35, 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, 36])
total number of confs: 166
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057202 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057202
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057202/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057202
Building REAL300000057203
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057203'
/scratch/stefan/7769638/working/building/REAL300000057203 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057203

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057203/0 /scratch/stefan/7769638/working/building/REAL300000057203 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 216)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/216
`/scratch/stefan/7769638/working/3D/216' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2CCC3)C=C1)

`REAL300000057203.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057203/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057203 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2CCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 16, 16, 16, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 9, 16, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1] 49
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057203 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2CCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 25, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 25, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48] 48
rigid atoms, others: [32, 33, 34, 35, 36, 37, 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, 38, 22, 23, 24, 25, 26, 27, 28, 39])
total number of confs: 133
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057203 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057203
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057203/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057203
Building REAL300000057204
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057204'
/scratch/stefan/7769638/working/building/REAL300000057204 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057204

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057204/0 /scratch/stefan/7769638/working/building/REAL300000057204 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 217)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/217
`/scratch/stefan/7769638/working/3D/217' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057204.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057204.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057204/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057204 none CC1=C(C)NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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]
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, 4, 4, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 2, 2, 2, 1, 4, 8, 20, 20, 20, 20, 20] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057204 none CC1=C(C)NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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]
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, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 5, 1, 1, 1, 1] 20
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 42
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057204 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057204
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057204/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057204
Building REAL300000057205
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057205'
/scratch/stefan/7769638/working/building/REAL300000057205 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057205

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057205/0 /scratch/stefan/7769638/working/building/REAL300000057205 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 218)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/218
`/scratch/stefan/7769638/working/3D/218' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC([N+](=O)[O-])=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057205.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057205.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057205/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057205 none COC1=CC([N+](=O)[O-])=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 1, 1, 11, 11, 11, 33, 33, 33, 84, 88, 88, 88, 88, 88, 88, 88, 88, 4, 4, 4, 1, 1, 1, 11, 11, 11, 33, 84, 88, 88, 88, 88] 88
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 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: 238
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057205 none COC1=CC([N+](=O)[O-])=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 85, 88, 88, 88, 88, 88, 37, 37, 37, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 88, 37, 37, 37, 14, 7, 1, 1, 1, 1] 88
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: 162
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057205 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057205
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057205/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057205
Building REAL300000057206
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057206'
/scratch/stefan/7769638/working/building/REAL300000057206 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057206

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057206/0 /scratch/stefan/7769638/working/building/REAL300000057206 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 219)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/219
`/scratch/stefan/7769638/working/3D/219' -> `0.mol2'
Preparing input files

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

`REAL300000057206.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057206.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057206/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057206 none CC(CC(C)(C)C#N)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 5, 5, 5, 5, 1, 8, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [33, 33, 33, 79, 145, 145, 145, 145, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 79, 79, 145, 145, 145, 145, 145, 145, 14, 7, 1, 1, 1, 1] 145
rigid atoms, others: [35, 36, 37, 38, 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])
total number of confs: 589
number of broken/clashed sets: 101
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057206 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057206
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057206/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057206
Building REAL300000057207
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057207'
/scratch/stefan/7769638/working/building/REAL300000057207 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057207

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057207/0 /scratch/stefan/7769638/working/building/REAL300000057207 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 220)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/220
`/scratch/stefan/7769638/working/3D/220' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCC1)

`REAL300000057207.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057207.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057207/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057207 none COC1(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H']
dock atom type numbers: [5, 12, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 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, 4, 7, 6, 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]
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, 1, 1, 11, 11, 11, 37, 37, 37, 70, 72, 72, 70, 71, 72, 72, 72, 72, 1, 1, 1, 6, 6, 6, 11, 11, 11, 37, 70, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1] 72
rigid atoms, others: [1, 2, 3, 36, 37, 35, 39, 34, 19, 20, 21, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 225
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057207 none COC1(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H']
dock atom type numbers: [5, 12, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 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, 4, 7, 6, 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]
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, 39, 39, 39, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 72, 72, 72, 72, 72, 72, 39, 39, 39, 14, 7, 1, 1, 1, 1, 72, 72, 72, 72, 72, 72] 72
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 182
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057207 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057207
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057207/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057207
Building REAL300000057208
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057208'
/scratch/stefan/7769638/working/building/REAL300000057208 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057208

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057208/0 /scratch/stefan/7769638/working/building/REAL300000057208 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 221)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/221
`/scratch/stefan/7769638/working/3D/221' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)N1N=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057208.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057208.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057208/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057208 none CC(C)(C)N1N=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 8, 31, 31, 31, 87, 97, 97, 90, 92, 97, 97, 97, 97, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 30, 87, 97, 97, 97, 97] 102
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23] set([0, 2, 3, 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])
total number of confs: 294
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057208 none CC(C)(C)N1N=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 97, 102, 102, 97, 97, 97, 55, 55, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 102, 102, 102, 102, 102, 102, 102, 102, 102, 55, 15, 7, 1, 1, 1, 1] 102
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 195
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057208 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057208
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057208/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057208
Building REAL300000057209
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057209'
/scratch/stefan/7769638/working/building/REAL300000057209 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057209

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057209/0 /scratch/stefan/7769638/working/building/REAL300000057209 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 222)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/222
`/scratch/stefan/7769638/working/3D/222' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057209.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057209/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057209 none CC(C)(C)NS(=O)(=O)C1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 7, 6, 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]
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: [6, 5, 6, 6, 5, 1, 5, 5, 1, 1, 8, 8, 16, 16, 16, 32, 33, 33, 32, 32, 33, 33, 33, 33, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 8, 16, 32, 33, 33, 33, 33, 1, 1, 1, 1] 56
rigid atoms, others: [5, 8, 9, 43, 44, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 6, 7, 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, 40, 41, 42])
total number of confs: 119
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057209 none CC(C)(C)NS(=O)(=O)C1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 7, 6, 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]
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, 33, 56, 56, 12, 12, 9, 9, 6, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 12, 9, 6, 1, 1, 1, 1, 33, 33, 33, 33] 56
rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46])
total number of confs: 210
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057209 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057209
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057209/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057209
Building REAL300000057210
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057210'
/scratch/stefan/7769638/working/building/REAL300000057210 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057210

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057210/0 /scratch/stefan/7769638/working/building/REAL300000057210 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 223)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/223
`/scratch/stefan/7769638/working/3D/223' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NNC2=CS(=O)(=O)CC3=CC=CC=C32)C=C1)

`REAL300000057210.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057210.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057210/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057210 none O=C([O-])C1=CC=C(NC(=O)NNC2=CS(=O)(=O)CC3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 21, 21, 21, 66, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 1, 1, 1, 1, 8, 21, 66, 150, 150, 150, 150, 150, 150, 150, 1, 1] 150
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 294
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057210 none O=C([O-])C1=CC=C(NC(=O)NNC2=CS(=O)(=O)CC3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [198, 198, 198, 198, 198, 198, 195, 59, 59, 59, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 195, 59, 10, 1, 1, 1, 1, 1, 1, 1, 198, 198] 198
rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 38, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 521
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057210 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057210
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057210/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057210
Building REAL300000057211
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057211'
/scratch/stefan/7769638/working/building/REAL300000057211 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057211

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057211/0 /scratch/stefan/7769638/working/building/REAL300000057211 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 224)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/224
`/scratch/stefan/7769638/working/3D/224' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057211.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057211.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057211/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057211 none COC1=CC=CC(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 27, 27, 27, 75, 78, 78, 75, 75, 78, 78, 78, 78, 3, 3, 3, 1, 1, 1, 13, 27, 75, 78, 78, 78, 78] 78
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 231
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057211 none COC1=CC=CC(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 58, 78, 78, 78, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 34, 16, 7, 1, 1, 1, 1] 78
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])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057211 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057211
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057211/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057211
Building REAL300000057212
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057212'
/scratch/stefan/7769638/working/building/REAL300000057212 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057212

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057212/0 /scratch/stefan/7769638/working/building/REAL300000057212 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 225)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/225
`/scratch/stefan/7769638/working/3D/225' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CN=CC=C2O1)

`REAL300000057212.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057212.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057212/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057212 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CN=CC=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.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, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 12, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 18, 10, 7, 1, 1, 1, 1, 26, 26, 26, 26] 26
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 55
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057212 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CN=CC=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.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, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 12, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [8, 1, 8, 8, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 12, 26, 26, 26, 26, 26, 1, 1, 1, 1] 26
rigid atoms, others: [1, 34, 35, 36, 37, 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])
total number of confs: 69
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057212 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057212
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057212/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057212
Building REAL300000057213
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057213'
/scratch/stefan/7769638/working/building/REAL300000057213 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057213

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057213/0 /scratch/stefan/7769638/working/building/REAL300000057213 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 226)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/226
`/scratch/stefan/7769638/working/3D/226' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1)

`REAL300000057213.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057213.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057213/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057213 none CCCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 22, 6, 1, 1, 1, 1, 1, 1, 13, 13, 29, 29, 29, 62, 75, 75, 68, 75, 75, 75, 75, 75, 1, 1, 1, 40, 40, 40, 40, 40, 22, 22, 1, 1, 13, 29, 62, 75, 75, 75, 75, 2, 2, 2, 1] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 45, 23, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 398
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057213 none CCCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
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, 26, 26, 75, 75, 26, 26, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 201, 201, 201, 201, 201, 201, 201, 75, 75, 26, 10, 6, 1, 1, 1, 1, 75, 75, 75, 75] 201
rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 598
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057213 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057213
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057213/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057213
Building REAL300000057214
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057214'
/scratch/stefan/7769638/working/building/REAL300000057214 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057214

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057214/0 /scratch/stefan/7769638/working/building/REAL300000057214 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 227)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/227
`/scratch/stefan/7769638/working/3D/227' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=NC=C3S2)C=C1)

`REAL300000057214.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057214/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057214 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=NC=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 1, 1, 7, 7, 6, 6, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 11, 11, 11, 28, 28, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 10, 11, 28, 37, 37, 37, 37, 1, 1] 37
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 22, 23, 24, 25, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057214 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=NC=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 1, 1, 7, 7, 6, 6, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 17, 17, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 16, 8, 1, 1, 1, 1, 37, 37] 37
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, 34, 33, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057214 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057214
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057214/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057214
Building REAL300000057215
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057215'
/scratch/stefan/7769638/working/building/REAL300000057215 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057215

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057215/0 /scratch/stefan/7769638/working/building/REAL300000057215 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 228)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/228
`/scratch/stefan/7769638/working/3D/228' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC=CC=C2N1C)

`REAL300000057215.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057215.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057215/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057215 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC=CC=C2N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'N.pl3', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 29, 30, 30, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 29, 58, 58, 58, 58, 58, 1, 1, 1, 1, 2, 2, 2] 58
rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 171
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057215 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC=CC=C2N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'N.pl3', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 32, 32, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 32, 12, 7, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58] 58
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 101
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057215 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057215
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057215/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057215
Building REAL300000057216
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057216'
/scratch/stefan/7769638/working/building/REAL300000057216 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057216

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057216/0 /scratch/stefan/7769638/working/building/REAL300000057216 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 229)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/229
`/scratch/stefan/7769638/working/3D/229' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C3CCCN3N=C2)C=C1)

`REAL300000057216.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057216.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057216/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057216 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C3CCCN3N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 15, 15, 15, 37, 37, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 8, 15, 37, 56, 56, 56, 56, 56, 56, 56, 1, 1] 56
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057216 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C3CCCN3N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 24, 7, 1, 1, 1, 1, 1, 1, 1, 55, 55] 55
rigid atoms, others: [32, 33, 34, 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, 11, 35, 21, 22, 23, 24, 25, 26, 27, 36])
total number of confs: 147
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057216 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057216
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057216/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057216
Building REAL300000057217
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057217'
/scratch/stefan/7769638/working/building/REAL300000057217 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057217

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057217/0 /scratch/stefan/7769638/working/building/REAL300000057217 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 230)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/230
`/scratch/stefan/7769638/working/3D/230' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC(F)=C(Cl)C=C32)C=C1)

`REAL300000057217.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057217.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057217/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057217 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC(F)=C(Cl)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 12, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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
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, 8, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 8, 12, 19, 19, 19, 19, 19, 19, 1, 1] 19
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: 46
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057217 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC(F)=C(Cl)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 12, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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
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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 19, 19] 19
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 37, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 49
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057217 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057217
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057217/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057217
Building REAL300000057218
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057218'
/scratch/stefan/7769638/working/building/REAL300000057218 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057218

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057218/0 /scratch/stefan/7769638/working/building/REAL300000057218 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 231)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/231
`/scratch/stefan/7769638/working/3D/231' -> `0.mol2'
Preparing input files

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

`REAL300000057218.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057218.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057218/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057218 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(C)C1=CC=C(CC(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 80, 80, 124, 124, 90, 98, 201, 192, 201, 124, 124, 30, 30, 30, 15, 7, 1, 1, 1, 1, 80, 80, 80, 80, 124, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124] 201
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 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, 50, 51, 52, 53])
total number of confs: 980
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057218 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(C)C1=CC=C(CC(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 51, 51, 51, 113, 124, 124, 113, 113, 124, 124, 124, 124, 1, 7, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 23, 23, 23, 51, 113, 124, 124, 124, 124, 7, 7, 7, 7, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1] 201
rigid atoms, others: [41, 42, 16, 18, 19, 20, 21, 22, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 471
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057218 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057218
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057218/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057218
Building REAL300000057219
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057219'
/scratch/stefan/7769638/working/building/REAL300000057219 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057219

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057219/0 /scratch/stefan/7769638/working/building/REAL300000057219 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 232)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/232
`/scratch/stefan/7769638/working/3D/232' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C2OC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC2=CC=C1)

`REAL300000057219.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057219.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057219/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057219 none CCC1=C2OC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC2=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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]
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: [6, 1, 1, 1, 1, 1, 1, 9, 9, 28, 28, 28, 54, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 27, 54, 56, 56, 56, 56, 1, 1, 1, 1] 88
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 41, 21, 22, 23, 24, 25, 38] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057219 none CCC1=C2OC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC2=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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]
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, 56, 56, 56, 56, 40, 40, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 56, 56, 56, 56, 56, 88, 88, 88, 88, 88, 40, 14, 7, 1, 1, 1, 1, 56, 56, 56, 56] 88
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 299
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057219 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057219
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057219/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057219
Building REAL300000057220
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057220'
/scratch/stefan/7769638/working/building/REAL300000057220 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057220

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057220/0 /scratch/stefan/7769638/working/building/REAL300000057220 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 233)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/233
`/scratch/stefan/7769638/working/3D/233' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Br)C=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057220.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057220.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057220/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057220 none CC1=C(Br)C=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 17, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 1, 12, 12, 24, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 2, 2, 2, 1, 1, 12, 24, 40, 40, 40, 40, 40] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057220 none CC1=C(Br)C=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 17, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 40, 24, 24, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 40, 40, 24, 10, 7, 1, 1, 1, 1] 40
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057220 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057220
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057220/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057220
Building REAL300000057221
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057221'
/scratch/stefan/7769638/working/building/REAL300000057221 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057221

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057221/0 /scratch/stefan/7769638/working/building/REAL300000057221 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 234)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/234
`/scratch/stefan/7769638/working/3D/234' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(CC1CCOCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057221.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057221.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057221/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057221 none COCC(CC1CCOCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 5, 5, 5, 5, 12, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [123, 83, 29, 8, 1, 1, 1, 1, 1, 1, 1, 29, 29, 57, 57, 57, 124, 145, 145, 124, 137, 145, 145, 145, 145, 123, 123, 123, 83, 83, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 124, 145, 145, 145, 145] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 36, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46])
total number of confs: 836
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057221 none COCC(CC1CCOCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 5, 5, 5, 5, 12, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 64, 18, 18, 18, 92, 145, 145, 145, 145, 145, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 89, 89, 89, 64, 64, 92, 92, 145, 145, 145, 145, 145, 145, 145, 145, 145, 8, 6, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 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, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 722
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057221 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057221
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057221/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057221
Building REAL300000057222
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057222'
/scratch/stefan/7769638/working/building/REAL300000057222 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057222

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057222/0 /scratch/stefan/7769638/working/building/REAL300000057222 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 235)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/235
`/scratch/stefan/7769638/working/3D/235' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl)

`REAL300000057222.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057222.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057222/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057222 none COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 8, 8, 30, 31, 31, 83, 94, 94, 83, 83, 94, 94, 94, 94, 1, 1, 1, 7, 7, 7, 1, 1, 8, 30, 83, 94, 94, 94, 94, 1] 119
rigid atoms, others: [2, 4, 5, 6, 7, 8, 23, 24, 25, 38, 29, 30] set([0, 1, 3, 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: 338
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057222 none COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [119, 119, 94, 119, 94, 94, 94, 42, 42, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 94, 94, 94, 119, 119, 119, 94, 94, 42, 16, 7, 1, 1, 1, 1, 94] 119
rigid atoms, others: [34, 35, 36, 37, 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, 38])
total number of confs: 261
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057222 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057222
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057222/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057222
Building REAL300000057223
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057223'
/scratch/stefan/7769638/working/building/REAL300000057223 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057223

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057223/0 /scratch/stefan/7769638/working/building/REAL300000057223 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 236)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/236
`/scratch/stefan/7769638/working/3D/236' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1)

`REAL300000057223.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057223/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057223 none C=CCCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 18, 8, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 49, 63, 63, 49, 49, 63, 63, 63, 63, 1, 1, 51, 51, 51, 18, 18, 8, 8, 1, 7, 20, 49, 63, 63, 63, 63] 201
rigid atoms, others: [3, 4, 5, 6, 7, 22, 23, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 412
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057223 none C=CCCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 145, 62, 62, 62, 39, 39, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 62, 62, 201, 201, 201, 201, 201, 145, 145, 62, 39, 16, 7, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 782
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057223 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057223
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057223/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057223
Building REAL300000057224
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057224'
/scratch/stefan/7769638/working/building/REAL300000057224 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057224

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057224/0 /scratch/stefan/7769638/working/building/REAL300000057224 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 237)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/237
`/scratch/stefan/7769638/working/3D/237' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN3CCCC3=C2)C=C1)

`REAL300000057224.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057224.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057224/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057224 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN3CCCC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 6, 8, 8, 8, 24, 24, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 6, 8, 24, 26, 26, 26, 26, 26, 26, 26, 1, 1] 26
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 50
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057224 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN3CCCC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 13, 12, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 12, 6, 1, 1, 1, 1, 1, 1, 1, 28, 28] 28
rigid atoms, others: [32, 33, 34, 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, 11, 35, 21, 22, 23, 24, 25, 26, 27, 36])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057224 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057224
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057224/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057224
Building REAL300000057225
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057225'
/scratch/stefan/7769638/working/building/REAL300000057225 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057225

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057225/0 /scratch/stefan/7769638/working/building/REAL300000057225 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 238)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/238
`/scratch/stefan/7769638/working/3D/238' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CC2CC2)C=C1)

`REAL300000057225.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057225.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057225/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057225 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CC2CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 13, 13, 13, 32, 32, 98, 98, 98, 98, 98, 167, 201, 201, 1, 1, 1, 1, 9, 13, 32, 98, 98, 167, 167, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 648
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057225 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CC2CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 80, 72, 80, 80, 66, 28, 28, 28, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 80, 80, 80, 80, 66, 28, 9, 1, 1, 5, 5, 22, 22, 22, 22, 22, 80, 80] 160
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 305
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057225 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CC2CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [160, 160, 160, 160, 160, 160, 159, 104, 104, 104, 58, 58, 22, 22, 22, 22, 22, 9, 1, 1, 1, 1, 160, 160, 160, 160, 159, 104, 58, 22, 22, 9, 9, 1, 1, 1, 1, 1, 160, 160] 160
rigid atoms, others: [33, 34, 35, 36, 37, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39])
total number of confs: 480
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057225 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057225
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057225/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057225
Building REAL300000057226
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057226'
/scratch/stefan/7769638/working/building/REAL300000057226 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057226

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057226/0 /scratch/stefan/7769638/working/building/REAL300000057226 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 239)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/239
`/scratch/stefan/7769638/working/3D/239' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3CC3)=C2F)C=C1)

`REAL300000057226.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057226.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057226/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057226 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3CC3)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 15, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 17, 17, 17, 42, 42, 86, 86, 86, 86, 86, 188, 201, 201, 86, 86, 1, 1, 1, 1, 8, 17, 42, 86, 86, 86, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 353
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057226 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3CC3)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 15, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [87, 81, 87, 77, 87, 87, 76, 33, 32, 33, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 37, 37, 1, 1, 87, 87, 87, 87, 76, 32, 12, 1, 1, 1, 37, 37, 37, 37, 37, 87, 87] 201
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 375
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057226 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3CC3)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 15, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 201, 201, 200, 140, 140, 140, 93, 93, 37, 37, 37, 37, 37, 10, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 200, 140, 93, 37, 37, 37, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40])
total number of confs: 545
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057226 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057226
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057226/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057226
Building REAL300000057227
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057227'
/scratch/stefan/7769638/working/building/REAL300000057227 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057227

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057227/0 /scratch/stefan/7769638/working/building/REAL300000057227 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 240)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/240
`/scratch/stefan/7769638/working/3D/240' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1)

`REAL300000057227.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057227.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057227/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057227 none CCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 2, 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
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [17, 7, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 35, 77, 90, 90, 86, 90, 90, 90, 90, 90, 1, 1, 1, 17, 17, 17, 17, 17, 1, 1, 12, 35, 77, 90, 90, 90, 90, 2, 2, 2, 1] 131
rigid atoms, others: [2, 3, 4, 5, 6, 7, 42, 22, 23, 24, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 307
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057227 none CCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 2, 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
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [131, 119, 43, 40, 90, 90, 40, 40, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 90, 90, 90, 131, 131, 131, 131, 131, 90, 90, 40, 17, 7, 1, 1, 1, 1, 90, 90, 90, 90] 131
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 411
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057227 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057227
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057227/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057227
Building REAL300000057228
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057228'
/scratch/stefan/7769638/working/building/REAL300000057228 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057228

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057228/0 /scratch/stefan/7769638/working/building/REAL300000057228 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 241)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/241
`/scratch/stefan/7769638/working/3D/241' -> `0.mol2'
Preparing input files

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

`REAL300000057228.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057228.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057228/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057228 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(F)=C2OC(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 1, 1, 7, 7, 6, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 21, 21, 21, 52, 52, 110, 110, 110, 110, 110, 110, 110, 191, 201, 201, 1, 1, 1, 1, 10, 21, 52, 110, 110, 110, 201, 1, 1] 201
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: 373
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057228 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(F)=C2OC(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 1, 1, 7, 7, 6, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 83, 76, 83, 83, 70, 24, 24, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 36, 36, 83, 83, 83, 83, 70, 24, 8, 1, 1, 1, 36, 83, 83] 169
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 348
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057228 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057228
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057228/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057228
Building REAL300000057229
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057229'
/scratch/stefan/7769638/working/building/REAL300000057229 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057229

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057229/0 /scratch/stefan/7769638/working/building/REAL300000057229 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 242)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/242
`/scratch/stefan/7769638/working/3D/242' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN(C(F)F)C2=O)C=C1)

`REAL300000057229.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057229.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057229/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057229 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN(C(F)F)C2=O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'F', 'F', 'C.2', 'O.2', '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, 11, 8, 8, 1, 1, 1, 1, 1, 8, 5, 15, 15, 1, 11, 1, 1, 7, 7, 6, 6, 7, 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, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 27, 27, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 8, 13, 27, 56, 56, 56, 56, 1, 1] 56
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: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057229 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN(C(F)F)C2=O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'F', 'F', 'C.2', 'O.2', '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, 11, 8, 8, 1, 1, 1, 1, 1, 8, 5, 15, 15, 1, 11, 1, 1, 7, 7, 6, 6, 7, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 47, 50, 46, 50, 50, 46, 22, 21, 22, 9, 9, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 50, 50, 50, 50, 46, 21, 9, 1, 1, 1, 8, 50, 50] 50
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 182
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057229 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057229
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057229/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057229
Building REAL300000057230
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057230'
/scratch/stefan/7769638/working/building/REAL300000057230 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057230

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057230/0 /scratch/stefan/7769638/working/building/REAL300000057230 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 243)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/243
`/scratch/stefan/7769638/working/3D/243' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2CCS(=O)(=O)CC2)C=C1)

`REAL300000057230.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057230.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057230/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057230 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCS(=O)(=O)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 14, 11, 11, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 14, 14, 14, 27, 27, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 10, 14, 27, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 134
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057230 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCS(=O)(=O)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 14, 11, 11, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 56, 31, 31, 31, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 56, 31, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58] 58
rigid atoms, others: [32, 33, 34, 35, 36, 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, 11, 38, 21, 22, 23, 24, 25, 26, 27, 37])
total number of confs: 159
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057230 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057230
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057230/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057230
Building REAL300000057231
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057231'
/scratch/stefan/7769638/working/building/REAL300000057231 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057231

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057231/0 /scratch/stefan/7769638/working/building/REAL300000057231 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 244)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/244
`/scratch/stefan/7769638/working/3D/244' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCS(=O)(=O)CC2)C=C1)

`REAL300000057231.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057231.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057231/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057231 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCS(=O)(=O)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 14, 11, 11, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 8, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 42
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057231 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCS(=O)(=O)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 14, 11, 11, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 18
rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 38, 37])
total number of confs: 45
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057231 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057231
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057231/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057231
Building REAL300000057232
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057232'
/scratch/stefan/7769638/working/building/REAL300000057232 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057232

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057232/0 /scratch/stefan/7769638/working/building/REAL300000057232 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 245)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/245
`/scratch/stefan/7769638/working/3D/245' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)C=C1)

`REAL300000057232.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057232.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057232/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057232 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 8, 1, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 10, 10, 10, 32, 32, 32, 32, 32, 81, 81, 81, 81, 81, 81, 81, 81, 32, 32, 1, 1, 1, 1, 8, 10, 32, 32, 32, 32, 81, 81, 81, 32, 32, 32, 32, 1, 1] 81
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 124
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057232 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 8, 1, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 32, 33, 32, 33, 33, 32, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 33, 33, 33, 33, 32, 10, 1, 1, 1, 1, 11, 11, 11, 1, 1, 1, 1, 33, 33] 82
rigid atoms, others: [33, 34, 35, 36, 40, 41, 10, 11, 12, 13, 14, 15, 16, 43, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 37, 38, 39, 44, 45])
total number of confs: 101
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057232 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 8, 1, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 81, 82, 81, 82, 82, 81, 42, 42, 42, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 11, 11, 82, 82, 82, 82, 81, 42, 11, 11, 11, 11, 1, 1, 1, 11, 11, 11, 11, 82, 82] 82
rigid atoms, others: [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, 36, 40, 41, 42, 43, 44, 45])
total number of confs: 225
number of broken/clashed sets: 48
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057232 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057232
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057232/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057232
Building REAL300000057233
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057233'
/scratch/stefan/7769638/working/building/REAL300000057233 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057233

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057233/0 /scratch/stefan/7769638/working/building/REAL300000057233 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 246)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/246
`/scratch/stefan/7769638/working/3D/246' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2CCN(C3=CC=CC=C3)C2)C=C1)

`REAL300000057233.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057233.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057233/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057233 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCN(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 16, 16, 16, 16, 16, 12, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 12, 12, 1, 1] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 44, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057233 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCN(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [72, 71, 72, 71, 72, 72, 70, 32, 31, 32, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 72, 72, 72, 72, 70, 31, 12, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 72, 72] 116
rigid atoms, others: [32, 33, 34, 35, 41, 42, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057233 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCN(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [116, 116, 116, 116, 116, 116, 115, 56, 56, 56, 25, 25, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 116, 116, 116, 116, 115, 56, 25, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 116, 116] 116
rigid atoms, others: [36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44])
total number of confs: 324
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057233 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057233
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057233/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057233
Building REAL300000057234
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057234'
/scratch/stefan/7769638/working/building/REAL300000057234 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057234

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057234/0 /scratch/stefan/7769638/working/building/REAL300000057234 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 247)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/247
`/scratch/stefan/7769638/working/3D/247' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2C3CC4CC(C3)CC2C4)C=C1)

`REAL300000057234.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057234.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057234/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057234 none O=C([O-])C1=CC=C(NC(=O)NN=CC2C3CC4CC(C3)CC2C4)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 28, 28, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 10, 14, 28, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1] 58
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 46, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 147
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057234 none O=C([O-])C1=CC=C(NC(=O)NN=CC2C3CC4CC(C3)CC2C4)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 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, 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, 24, 23, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62] 62
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, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 45, 46, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 171
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057234 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057234
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057234/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057234
Building REAL300000057235
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057235'
/scratch/stefan/7769638/working/building/REAL300000057235 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057235

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057235/0 /scratch/stefan/7769638/working/building/REAL300000057235 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 248)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/248
`/scratch/stefan/7769638/working/3D/248' -> `0.mol2'
Preparing input files

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

`REAL300000057235.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057235.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057235/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057235 none O=C([O-])C1=CC=C(NC(=O)NN=C(CCC(F)(F)F)CCC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 11, 8, 8, 1, 5, 5, 5, 15, 15, 15, 5, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 6, 6, 22, 22, 68, 82, 84, 84, 84, 22, 117, 145, 145, 145, 145, 1, 1, 1, 1, 6, 6, 68, 68, 84, 84, 117, 117, 145, 145, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 25, 26, 27, 28] set([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: 845
number of broken/clashed sets: 109
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057235 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057235
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057235/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057235
Building REAL300000057236
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057236'
/scratch/stefan/7769638/working/building/REAL300000057236 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057236

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057236/0 /scratch/stefan/7769638/working/building/REAL300000057236 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 249)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/249
`/scratch/stefan/7769638/working/3D/249' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC=C(Cl)N1C)

`REAL300000057236.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057236.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057236/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057236 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC=C(Cl)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'N.pl3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 16, 8, 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, 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
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 1, 1, 1, 1, 20, 20, 20, 20] 20
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 41
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057236 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC=C(Cl)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'N.pl3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 16, 8, 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, 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
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 11, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 20, 20, 20, 20, 20, 1, 2, 2, 2] 20
rigid atoms, others: [32, 1, 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, 33, 34, 35])
total number of confs: 67
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057236 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057236
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057236/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057236
Building REAL300000057237
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057237'
/scratch/stefan/7769638/working/building/REAL300000057237 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057237

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057237/0 /scratch/stefan/7769638/working/building/REAL300000057237 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 250)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/250
`/scratch/stefan/7769638/working/3D/250' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2COC3(CCC3)C2)C=C1)

`REAL300000057237.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057237.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057237/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057237 none O=C([O-])C1=CC=C(NC(=O)NN=C2COC3(CCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 8, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1] 22
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 36, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057237 none O=C([O-])C1=CC=C(NC(=O)NN=C2COC3(CCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 22
rigid atoms, others: [32, 33, 34, 35, 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, 8, 9, 20, 21, 22, 23, 24, 25, 37, 36])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057237 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057237
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057237/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057237
Building REAL300000057238
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057238'
/scratch/stefan/7769638/working/building/REAL300000057238 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057238

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057238/0 /scratch/stefan/7769638/working/building/REAL300000057238 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 251)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/251
`/scratch/stefan/7769638/working/3D/251' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(=C3CCC3)CC2)C=C1)

`REAL300000057238.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057238.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057238/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057238 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(=C3CCC3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 8, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1] 34
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 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, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 64
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057238 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(=C3CCC3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 32, 34, 34, 32, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 34
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 43, 22, 23, 24, 25, 26, 27])
total number of confs: 93
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057238 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(=C3CCC3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 32, 34, 34, 32, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 34
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 43, 22, 23, 24, 25, 26, 27])
total number of confs: 93
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057238 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057238
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057238/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057238
Building REAL300000057239
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057239'
/scratch/stefan/7769638/working/building/REAL300000057239 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057239

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057239/0 /scratch/stefan/7769638/working/building/REAL300000057239 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 252)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/252
`/scratch/stefan/7769638/working/3D/252' -> `0.mol2'
Preparing input files

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

`REAL300000057239.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057239.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057239/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057239 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC=C2OC(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 6, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 11, 16, 16, 16, 39, 39, 102, 102, 102, 55, 102, 102, 102, 171, 201, 201, 1, 1, 1, 1, 11, 16, 39, 102, 55, 102, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 24, 25, 26, 27, 36] set([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: 537
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057239 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC=C2OC(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 6, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 77, 66, 77, 77, 61, 26, 26, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 38, 38, 77, 77, 77, 77, 61, 26, 8, 1, 1, 1, 38, 77, 77] 201
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 366
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057239 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057239
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057239/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057239
Building REAL300000057240
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057240'
/scratch/stefan/7769638/working/building/REAL300000057240 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057240

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057240/0 /scratch/stefan/7769638/working/building/REAL300000057240 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 253)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/253
`/scratch/stefan/7769638/working/3D/253' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CN=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057240.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057240.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057240/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057240 none COC1=CN=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 51, 53, 53, 51, 52, 53, 53, 53, 53, 1, 3, 3, 3, 1, 1, 7, 27, 51, 53, 53, 53, 53, 1] 60
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 22, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 164
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057240 none COC1=CN=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [60, 53, 53, 53, 53, 53, 26, 26, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 60, 60, 60, 53, 53, 26, 12, 7, 1, 1, 1, 1, 53] 60
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 108
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057240 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057240
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057240/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057240
Building REAL300000057241
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057241'
/scratch/stefan/7769638/working/building/REAL300000057241 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057241

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057241/0 /scratch/stefan/7769638/working/building/REAL300000057241 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 254)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/254
`/scratch/stefan/7769638/working/3D/254' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)N1C=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057241.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057241.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057241/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057241 none CC(C)N1C=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 31, 34, 34, 31, 31, 34, 34, 34, 34, 6, 6, 6, 5, 6, 6, 6, 1, 1, 4, 14, 31, 34, 34, 34, 34] 34
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057241 none CC(C)N1C=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 24, 24, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 24, 16, 7, 1, 1, 1, 1] 34
rigid atoms, others: [35, 36, 37, 38, 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])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057241 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057241
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057241/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057241
Building REAL300000057242
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057242'
/scratch/stefan/7769638/working/building/REAL300000057242 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057242

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057242/0 /scratch/stefan/7769638/working/building/REAL300000057242 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 255)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/255
`/scratch/stefan/7769638/working/3D/255' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC3(C2)CCOCC3)C=C1)

`REAL300000057242.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057242.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057242/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057242 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3(C2)CCOCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 9, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057242 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3(C2)CCOCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 23
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, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 40, 21, 22, 23, 24, 25, 26])
total number of confs: 59
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057242 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057242
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057242/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057242
Building REAL300000057243
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057243'
/scratch/stefan/7769638/working/building/REAL300000057243 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057243

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057243/0 /scratch/stefan/7769638/working/building/REAL300000057243 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 256)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/256
`/scratch/stefan/7769638/working/3D/256' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC1=CC=C(Cl)C=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057243.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057243.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057243/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057243 none CCC(CC1=CC=C(Cl)C=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [43, 19, 3, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 67, 67, 67, 142, 155, 155, 142, 151, 155, 155, 155, 155, 43, 43, 43, 43, 43, 3, 3, 1, 1, 1, 1, 67, 142, 155, 155, 155, 155] 195
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 621
number of broken/clashed sets: 109
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057243 none CCC(CC1=CC=C(Cl)C=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [75, 42, 42, 42, 139, 155, 155, 155, 155, 155, 155, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 139, 139, 155, 155, 155, 155, 18, 7, 1, 1, 1, 1] 195
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 661
number of broken/clashed sets: 109
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057243 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057243
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057243/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057243
Building REAL300000057244
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057244'
/scratch/stefan/7769638/working/building/REAL300000057244 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057244

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057244/0 /scratch/stefan/7769638/working/building/REAL300000057244 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 257)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/257
`/scratch/stefan/7769638/working/3D/257' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(CO)C=C2)C=C1)

`REAL300000057244.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057244.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057244/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057244 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(CO)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 11, 8, 8, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 39, 39, 41, 41, 39, 41, 52, 41, 41, 1, 1, 1, 1, 9, 15, 39, 41, 41, 52, 52, 156, 41, 41, 1, 1] 156
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057244 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(CO)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 11, 8, 8, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 38, 41, 41, 38, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 1, 8, 1, 1, 41, 41, 41, 41, 38, 17, 4, 1, 1, 8, 8, 24, 1, 1, 41, 41] 156
rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 35, 36])
total number of confs: 166
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057244 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057244
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057244/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057244
Building REAL300000057245
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057245'
/scratch/stefan/7769638/working/building/REAL300000057245 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057245

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057245/0 /scratch/stefan/7769638/working/building/REAL300000057245 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 258)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/258
`/scratch/stefan/7769638/working/3D/258' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=CC(Br)=C1)

`REAL300000057245.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057245.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057245/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057245 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=CC(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 17, 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, 2, 2, 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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 70, 70, 70, 70, 70, 70, 32, 32, 32, 16, 7, 1, 1, 1, 1, 70, 70, 70] 70
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 34, 33, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 120
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057245 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=CC(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 17, 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, 2, 2, 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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 39, 40, 40, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 39, 70, 70, 70, 70, 70, 1, 1, 1] 70
rigid atoms, others: [32, 1, 34, 33, 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])
total number of confs: 189
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057245 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057245
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057245/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057245
Building REAL300000057246
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057246'
/scratch/stefan/7769638/working/building/REAL300000057246 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057246

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057246/0 /scratch/stefan/7769638/working/building/REAL300000057246 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 259)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/259
`/scratch/stefan/7769638/working/3D/259' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057246.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057246.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057246/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057246 none COC1=NC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 1, 1, 6, 10, 22, 22, 22, 22, 22] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28] set([9, 10, 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: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057246 none COC1=NC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 22, 22, 22, 22, 22, 22, 22, 12, 7, 1, 1, 1, 1] 22
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: 48
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057246 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057246
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057246/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057246
Building REAL300000057247
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057247'
/scratch/stefan/7769638/working/building/REAL300000057247 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057247

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057247/0 /scratch/stefan/7769638/working/building/REAL300000057247 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 260)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/260
`/scratch/stefan/7769638/working/3D/260' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(O)=C2F)C=C1)

`REAL300000057247.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057247.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057247/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057247 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(O)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 9, 9, 9, 22, 22, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 7, 9, 22, 26, 26, 26, 52, 1, 1] 52
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057247 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(O)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 15, 14, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 14, 8, 1, 1, 1, 2, 27, 27] 54
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 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
/scratch/stefan/7769638/working/building/REAL300000057247 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057247
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057247/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057247
Building REAL300000057248
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057248'
/scratch/stefan/7769638/working/building/REAL300000057248 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057248

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057248/0 /scratch/stefan/7769638/working/building/REAL300000057248 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 261)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/261
`/scratch/stefan/7769638/working/3D/261' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC(CF)(CF)C2)C=C1)

`REAL300000057248.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057248.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057248/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057248 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(CF)(CF)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'C.3', '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, 11, 8, 8, 1, 5, 5, 5, 15, 5, 15, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 1, 1, 9, 12, 12, 12, 36, 36, 36, 36, 66, 36, 67, 36, 1, 1, 1, 1, 9, 12, 36, 36, 66, 66, 67, 67, 36, 36, 1, 1] 67
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 20, 21, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057248 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(CF)(CF)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'C.3', '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, 11, 8, 8, 1, 5, 5, 5, 15, 5, 15, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 36, 36, 26, 10, 9, 10, 1, 1, 1, 1, 1, 1, 9, 1, 6, 1, 36, 36, 36, 36, 26, 9, 1, 1, 9, 9, 6, 6, 1, 1, 36, 36] 67
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 17, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35])
total number of confs: 194
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057248 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057248
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057248/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057248
Building REAL300000057249
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057249'
/scratch/stefan/7769638/working/building/REAL300000057249 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057249

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057249/0 /scratch/stefan/7769638/working/building/REAL300000057249 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 262)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/262
`/scratch/stefan/7769638/working/3D/262' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN2CCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=O)C=C1)

`REAL300000057249.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057249.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057249/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057249 none COC1=CC=C(CN2CCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)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.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 30, 30, 30, 30, 30, 75, 76, 76, 195, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 75, 195, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 46, 47, 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])
total number of confs: 530
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057249 none COC1=CC=C(CN2CCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)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.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 18, 9, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 25, 34, 34, 29, 34, 34, 34, 34, 34, 1, 1, 30, 30, 30, 30, 30, 30, 30, 9, 9, 1, 1, 1, 1, 5, 25, 34, 34, 34, 34, 30, 30] 201
rigid atoms, others: [11, 36, 37, 6, 7, 8, 9, 10, 39, 12, 25, 26, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057249 none COC1=CC=C(CN2CCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)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.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 149, 201, 201, 149, 34, 34, 34, 34, 34, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 201, 201, 201, 201, 201, 201, 201, 149, 149, 34, 34, 34, 34, 18, 7, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47])
total number of confs: 838
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057249 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057249
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057249/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057249
Building REAL300000057250
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057250'
/scratch/stefan/7769638/working/building/REAL300000057250 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057250

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057250/0 /scratch/stefan/7769638/working/building/REAL300000057250 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 263)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/263
`/scratch/stefan/7769638/working/3D/263' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)N1CCC(C)(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057250.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057250.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057250/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057250 none CCOC(=O)N1CCC(C)(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 42, 42, 42, 82, 96, 96, 82, 82, 95, 96, 96, 96, 1, 1, 22, 22, 22, 21, 21, 1, 1, 1, 1, 2, 2, 2, 13, 41, 82, 96, 96, 96, 96, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 46, 47, 48, 49, 35, 25, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 430
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057250 none CCOC(=O)N1CCC(C)(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 191, 164, 96, 164, 96, 96, 96, 15, 96, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 96, 96, 201, 201, 201, 201, 201, 96, 96, 96, 96, 96, 96, 96, 15, 6, 6, 1, 1, 1, 1, 96, 96, 96, 96] 201
rigid atoms, others: [42, 43, 44, 45, 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, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49])
total number of confs: 578
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057250 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057250
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057250/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057250
Building REAL300000057251
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057251'
/scratch/stefan/7769638/working/building/REAL300000057251 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057251

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057251/0 /scratch/stefan/7769638/working/building/REAL300000057251 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 264)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/264
`/scratch/stefan/7769638/working/3D/264' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCS(=O)CC2)C=C1)

`REAL300000057251.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057251.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057251/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057251 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCS(=O)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 14, 11, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 13, 13, 13, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 36, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057251 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCS(=O)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 14, 11, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 17, 18, 18, 18, 18, 17, 7, 6, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 18
rigid atoms, others: [32, 33, 34, 35, 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, 8, 9, 20, 21, 22, 23, 24, 25, 37, 36])
total number of confs: 54
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057251 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057251
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057251/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057251
Building REAL300000057252
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057252'
/scratch/stefan/7769638/working/building/REAL300000057252 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057252

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057252/0 /scratch/stefan/7769638/working/building/REAL300000057252 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 265)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/265
`/scratch/stefan/7769638/working/3D/265' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC([O-])=C(Cl)C=C32)C=C1)

`REAL300000057252.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057252.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057252/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057252 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC([O-])=C(Cl)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 20, 20, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 10, 20, 23, 23, 23, 1, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 24, 25, 26, 27] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057252 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC([O-])=C(Cl)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 7, 1, 1, 1, 23, 23] 23
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33, 24, 25, 26, 27, 28, 29])
total number of confs: 59
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057252 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057252/1 /scratch/stefan/7769638/working/building/REAL300000057252 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 266)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/266
`/scratch/stefan/7769638/working/3D/266' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC(O)=C(Cl)C=C32)C=C1)

`REAL300000057252.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057252.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057252/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057252 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC(O)=C(Cl)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 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, 1, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 12, 18, 18, 18, 36, 18, 1, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057252 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC(O)=C(Cl)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 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, 18, 18, 18, 4, 3, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 3, 1, 1, 2, 1, 18, 18] 36
rigid atoms, others: [33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 32, 24, 25, 26, 27, 28, 29])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057252 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057252
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057252/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057252/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057252
Building REAL300000057253
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057253'
/scratch/stefan/7769638/working/building/REAL300000057253 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057253

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057253/0 /scratch/stefan/7769638/working/building/REAL300000057253 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 267)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/267
`/scratch/stefan/7769638/working/3D/267' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3CCCC3)=C2)C=C1)

`REAL300000057253.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057253.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057253/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057253 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3CCCC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 15, 15, 9, 15, 15, 23, 23, 23, 23, 15, 1, 1, 1, 1, 3, 5, 5, 15, 15, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 15, 1, 1] 23
rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057253 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3CCCC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [90, 88, 90, 86, 90, 90, 81, 31, 30, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 90, 90, 90, 90, 81, 30, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 90, 90] 141
rigid atoms, others: [32, 33, 43, 12, 13, 14, 15, 16, 17, 18, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45])
total number of confs: 276
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057253 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3CCCC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 141, 141, 141, 138, 58, 58, 58, 26, 26, 6, 6, 5, 6, 6, 1, 1, 1, 1, 1, 1, 6, 141, 141, 141, 141, 138, 58, 26, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 141, 141] 141
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45])
total number of confs: 388
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057253 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057253
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057253/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057253
Building REAL300000057254
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057254'
/scratch/stefan/7769638/working/building/REAL300000057254 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057254

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057254/0 /scratch/stefan/7769638/working/building/REAL300000057254 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 268)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/268
`/scratch/stefan/7769638/working/3D/268' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(O)C(C(C)(C)C)=C1)

`REAL300000057254.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057254.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057254/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057254 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(O)C(C(C)(C)C)=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 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, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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, 6, 6, 14, 14, 14, 42, 50, 50, 42, 46, 50, 50, 50, 50, 1, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 1, 6, 14, 42, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 100
rigid atoms, others: [1, 2, 3, 4, 5, 49, 20, 21, 22, 23, 27, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 184
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057254 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(O)C(C(C)(C)C)=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 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, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [50, 50, 50, 50, 26, 26, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 16, 7, 1, 1, 1, 1, 100, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100
rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 191
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057254 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057254
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057254/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057254
Building REAL300000057255
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057255'
/scratch/stefan/7769638/working/building/REAL300000057255 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057255

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057255/0 /scratch/stefan/7769638/working/building/REAL300000057255 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 269)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/269
`/scratch/stefan/7769638/working/3D/269' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1)

`REAL300000057255.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057255.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057255/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057255 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 16, 16, 16, 37, 37, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 8, 16, 37, 71, 71, 71, 1, 1] 71
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 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])
total number of confs: 145
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057255 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 7, 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, 2, 2, 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, 59, 63, 59, 63, 63, 51, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 63, 63, 63, 63, 51, 19, 7, 1, 1, 1, 63, 63] 63
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057255 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057255
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057255/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057255
Building REAL300000057256
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057256'
/scratch/stefan/7769638/working/building/REAL300000057256 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057256

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057256/0 /scratch/stefan/7769638/working/building/REAL300000057256 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 270)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/270
`/scratch/stefan/7769638/working/3D/270' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F)

`REAL300000057256.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057256.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057256/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057256 none COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 8, 8, 26, 27, 27, 62, 76, 76, 70, 70, 76, 76, 76, 76, 1, 1, 1, 13, 13, 13, 1, 1, 8, 26, 62, 76, 76, 76, 76, 1] 104
rigid atoms, others: [2, 4, 5, 6, 7, 8, 23, 24, 25, 38, 29, 30] set([0, 1, 3, 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: 273
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057256 none COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 76, 104, 76, 76, 76, 36, 36, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 76, 76, 76, 104, 104, 104, 76, 76, 36, 12, 7, 1, 1, 1, 1, 76] 104
rigid atoms, others: [34, 35, 36, 37, 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, 38])
total number of confs: 226
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057256 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057256
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057256/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057256
Building REAL300000057257
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057257'
/scratch/stefan/7769638/working/building/REAL300000057257 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057257

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057257/0 /scratch/stefan/7769638/working/building/REAL300000057257 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 271)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/271
`/scratch/stefan/7769638/working/3D/271' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(C3CCC3)CC2)C=C1)

`REAL300000057257.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057257.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057257/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057257 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(C3CCC3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 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, 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, 1, 1, 1, 8, 14, 14, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 8, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 69
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057257 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(C3CCC3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 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, 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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 36, 36, 36, 36, 36, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 36, 36] 36
rigid atoms, others: [32, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 42, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 44, 45])
total number of confs: 95
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057257 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC(C3CCC3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 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, 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, 12, 12, 12, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 36, 36, 36, 36, 36, 12, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 36, 36] 36
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45])
total number of confs: 91
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057257 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057257
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057257/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057257
Building REAL300000057258
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057258'
/scratch/stefan/7769638/working/building/REAL300000057258 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057258

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057258/0 /scratch/stefan/7769638/working/building/REAL300000057258 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 272)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/272
`/scratch/stefan/7769638/working/3D/272' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C2=NN(C)C=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1)

`REAL300000057258.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057258.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057258/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057258 none CN1C=C(C2=NN(C)C=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 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, 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
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 46, 46, 99, 99, 99, 196, 197, 197, 197, 197, 197, 197, 197, 197, 1, 1, 2, 2, 2, 1, 12, 12, 12, 12, 46, 99, 196, 197, 197, 197, 197, 1] 197
rigid atoms, others: [0, 1, 2, 3, 4, 42, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 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])
total number of confs: 573
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057258 none CN1C=C(C2=NN(C)C=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 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, 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
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 31, 31, 31, 83, 92, 92, 88, 88, 92, 92, 92, 92, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 11, 31, 83, 92, 92, 92, 92, 12] 197
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057258 none CN1C=C(C2=NN(C)C=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 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, 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
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [197, 197, 197, 92, 92, 92, 92, 92, 92, 42, 42, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 197, 197, 197, 197, 197, 197, 92, 92, 92, 92, 42, 14, 7, 1, 1, 1, 1, 197] 197
rigid atoms, others: [38, 39, 40, 41, 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, 36, 37, 42])
total number of confs: 308
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057258 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057258
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057258/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057258
Building REAL300000057259
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057259'
/scratch/stefan/7769638/working/building/REAL300000057259 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057259

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057259/0 /scratch/stefan/7769638/working/building/REAL300000057259 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 273)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/273
`/scratch/stefan/7769638/working/3D/273' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=CSC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057259.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057259.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057259/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057259 none COCC1=CSC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 5, 1, 1, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 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, 7, 4, 7, 6, 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]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [33, 8, 1, 1, 1, 1, 1, 1, 9, 9, 28, 28, 28, 74, 88, 88, 78, 78, 88, 88, 88, 88, 1, 34, 34, 34, 8, 8, 1, 9, 28, 74, 88, 88, 88, 88, 1] 182
rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 36, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 361
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057259 none COCC1=CSC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 5, 1, 1, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 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, 7, 4, 7, 6, 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]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [182, 182, 88, 88, 88, 88, 46, 46, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 182, 182, 182, 182, 182, 88, 46, 18, 7, 1, 1, 1, 1, 88] 182
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: 594
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057259 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057259
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057259/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057259
Building REAL300000057260
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057260'
/scratch/stefan/7769638/working/building/REAL300000057260 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057260

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057260/0 /scratch/stefan/7769638/working/building/REAL300000057260 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 274)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/274
`/scratch/stefan/7769638/working/3D/274' -> `0.mol2'
Preparing input files

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

`REAL300000057260.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057260.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057260/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057260 none CC(CSCCF)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 14, 5, 5, 15, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 69, 141, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 69, 69, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 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])
total number of confs: 653
number of broken/clashed sets: 183
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057260 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057260
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057260/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057260
Building REAL300000057261
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057261'
/scratch/stefan/7769638/working/building/REAL300000057261 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057261

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057261/0 /scratch/stefan/7769638/working/building/REAL300000057261 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 275)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/275
`/scratch/stefan/7769638/working/3D/275' -> `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)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057261.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057261.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057261/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057261 none O=C([O-])C=CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [20, 12, 21, 12, 1, 1, 1, 1, 1, 1, 6, 6, 20, 21, 21, 62, 74, 74, 68, 74, 74, 74, 74, 74, 1, 12, 12, 1, 1, 6, 20, 61, 74, 74, 74, 74] 117
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])
total number of confs: 274
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057261 none O=C([O-])C=CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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, 74, 74, 74, 74, 45, 45, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 117, 117, 74, 74, 45, 16, 7, 1, 1, 1, 1] 117
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])
total number of confs: 269
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057261 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057261
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057261/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057261
Building REAL300000057262
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057262'
/scratch/stefan/7769638/working/building/REAL300000057262 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057262

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057262/0 /scratch/stefan/7769638/working/building/REAL300000057262 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 276)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/276
`/scratch/stefan/7769638/working/3D/276' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCSCC2)C=C1)

`REAL300000057262.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057262.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057262/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057262 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCSCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 14, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 10, 14, 14, 14, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 10, 14, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 36, 35] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 52
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057262 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCSCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 14, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 22
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 36, 35])
total number of confs: 57
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057262 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057262
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057262/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057262
Building REAL300000057263
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057263'
/scratch/stefan/7769638/working/building/REAL300000057263 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057263

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057263/0 /scratch/stefan/7769638/working/building/REAL300000057263 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 277)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/277
`/scratch/stefan/7769638/working/3D/277' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC1CCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057263.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057263.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057263/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057263 none C=CCC1CCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 44, 44, 37, 42, 44, 44, 44, 44, 19, 19, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 44, 44, 44, 44] 67
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42])
total number of confs: 197
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057263 none C=CCC1CCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 44, 44, 44, 44, 44, 44, 44, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 67, 67, 67, 67, 67, 44, 44, 44, 44, 44, 44, 44, 44, 44, 15, 7, 1, 1, 1, 1] 67
rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 195
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057263 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057263
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057263/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057263
Building REAL300000057264
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057264'
/scratch/stefan/7769638/working/building/REAL300000057264 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057264

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057264/0 /scratch/stefan/7769638/working/building/REAL300000057264 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 278)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/278
`/scratch/stefan/7769638/working/3D/278' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCC3)N=N2)C=C1)

`REAL300000057264.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057264.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057264/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057264 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCC3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 8, 8, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 16, 48, 48, 72, 72, 72, 121, 121, 121, 72, 72, 1, 1, 1, 1, 8, 16, 48, 72, 121, 121, 121, 121, 121, 121, 121, 1, 1] 121
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 287
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057264 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCC3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 8, 8, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 70, 75, 75, 66, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 11, 11, 11, 1, 1, 75, 75, 75, 75, 66, 26, 7, 1, 11, 11, 11, 11, 11, 11, 11, 75, 75] 126
rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 241
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057264 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCC3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 8, 8, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [126, 126, 126, 126, 126, 126, 125, 79, 79, 79, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 126, 126, 126, 126, 125, 79, 37, 11, 1, 1, 1, 1, 1, 1, 1, 126, 126] 126
rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38])
total number of confs: 338
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057264 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057264
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057264/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057264
Building REAL300000057265
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057265'
/scratch/stefan/7769638/working/building/REAL300000057265 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057265

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057265/0 /scratch/stefan/7769638/working/building/REAL300000057265 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 279)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/279
`/scratch/stefan/7769638/working/3D/279' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)C=C1)

`REAL300000057265.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057265.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057265/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057265 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 5, 5, 5, 5, 5, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 13, 13, 1, 1, 1, 1, 3, 5, 5, 13, 13, 33, 33, 33, 33, 13, 1, 1] 33
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057265 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 5, 4, 5, 4, 4, 1, 1, 1, 1, 1, 1, 6, 8, 8, 6, 6, 8, 8, 1, 1, 13, 13, 13, 13, 13, 4, 4, 1, 1, 8, 8, 8, 8, 1, 13, 13] 33
rigid atoms, others: [34, 35, 40, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057265 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 13, 13, 13, 13, 13, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 33, 33, 33, 33, 33, 13, 13, 8, 8, 1, 1, 1, 1, 8, 33, 33] 33
rigid atoms, others: [36, 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, 40, 41, 42])
total number of confs: 96
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057265 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057265
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057265/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057265
Building REAL300000057266
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057266'
/scratch/stefan/7769638/working/building/REAL300000057266 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057266

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057266/0 /scratch/stefan/7769638/working/building/REAL300000057266 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 280)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/280
`/scratch/stefan/7769638/working/3D/280' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C)

`REAL300000057266.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057266.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057266/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057266 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 57, 57, 57, 57, 57, 57, 57, 57, 57, 86, 88, 88, 24, 24, 24, 10, 6, 1, 1, 1, 1, 57, 57, 57, 88, 88, 88, 88, 88, 88, 88] 88
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 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])
total number of confs: 167
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057266 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 21, 21, 21, 47, 57, 57, 52, 52, 57, 57, 57, 57, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 17, 17, 7, 7, 7, 21, 47, 57, 57, 57, 57, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 88
rigid atoms, others: [1, 38, 39, 40, 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, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 239
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057266 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057266
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057266/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057266
Building REAL300000057267
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057267'
/scratch/stefan/7769638/working/building/REAL300000057267 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057267

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057267/0 /scratch/stefan/7769638/working/building/REAL300000057267 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 281)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/281
`/scratch/stefan/7769638/working/3D/281' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1C)

`REAL300000057267.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057267.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057267/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057267 none CC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 5, 5, 17, 18, 18, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 2, 2, 2, 1, 5, 17, 52, 52, 52, 52, 52, 2, 2, 2] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057267 none CC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 32, 32, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 32, 10, 5, 1, 1, 1, 1, 52, 52, 52] 52
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057267 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057267
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057267/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057267
Building REAL300000057268
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057268'
/scratch/stefan/7769638/working/building/REAL300000057268 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057268

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057268/0 /scratch/stefan/7769638/working/building/REAL300000057268 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 282)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/282
`/scratch/stefan/7769638/working/3D/282' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2S1)

`REAL300000057268.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057268.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057268/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057268 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 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, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24, 24, 12, 7, 1, 1, 1, 1, 33, 33, 33, 33] 33
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 63
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057268 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 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, 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
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, 21, 22, 22, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 21, 33, 33, 33, 33, 33, 1, 1, 1, 1] 33
rigid atoms, others: [1, 34, 35, 36, 37, 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])
total number of confs: 95
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057268 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057268
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057268/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057268
Building REAL300000057269
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057269'
/scratch/stefan/7769638/working/building/REAL300000057269 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057269

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057269/0 /scratch/stefan/7769638/working/building/REAL300000057269 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 283)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/283
`/scratch/stefan/7769638/working/3D/283' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C(C2=CC=CC=C2)=C1)

`REAL300000057269.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057269.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057269/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057269 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C(C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 34, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 34, 34, 34, 16, 7, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57] 57
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 108
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057269 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C(C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 11, 11, 24, 24, 24, 49, 57, 57, 52, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 11, 11, 11, 24, 49, 57, 57, 57, 57, 2, 2, 2, 4, 4, 1, 4, 4, 1] 57
rigid atoms, others: [1, 45, 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, 39, 40, 41, 42, 43, 44])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057269 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C(C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [21, 4, 21, 21, 32, 32, 32, 54, 57, 57, 57, 57, 57, 57, 57, 57, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 21, 21, 21, 32, 54, 57, 57, 57, 57, 4, 4, 4, 1, 1, 1, 1, 1, 4] 57
rigid atoms, others: [40, 41, 42, 43, 44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45])
total number of confs: 165
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057269 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057269
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057269/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057269
Building REAL300000057270
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057270'
/scratch/stefan/7769638/working/building/REAL300000057270 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057270

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057270/0 /scratch/stefan/7769638/working/building/REAL300000057270 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 284)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/284
`/scratch/stefan/7769638/working/3D/284' -> `0.mol2'
Preparing input files

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

`REAL300000057270.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057270.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057270/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057270 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(N)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.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.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 9, 9, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 5, 3, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9] 13
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 49
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057270 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(N)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.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.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 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]
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: [5, 3, 1, 3, 3, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 4, 9, 9, 9, 9, 9, 1, 1, 2, 2, 1, 1] 13
rigid atoms, others: [2, 35, 36, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 40
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057270 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057270
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057270/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057270
Building REAL300000057271
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057271'
/scratch/stefan/7769638/working/building/REAL300000057271 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057271

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057271/0 /scratch/stefan/7769638/working/building/REAL300000057271 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 285)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/285
`/scratch/stefan/7769638/working/3D/285' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CSC(C(F)(F)F)=C2)C=C1)

`REAL300000057271.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057271.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057271/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057271 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CSC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', '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, 11, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 37, 37, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 8, 14, 37, 61, 61, 1, 1] 61
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057271 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CSC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', '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, 11, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 60, 61, 60, 61, 61, 60, 28, 27, 28, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 61, 61, 61, 61, 60, 27, 9, 1, 1, 61, 61] 61
rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 178
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057271 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057271
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057271/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057271
Building REAL300000057272
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057272'
/scratch/stefan/7769638/working/building/REAL300000057272 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057272

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057272/0 /scratch/stefan/7769638/working/building/REAL300000057272 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 286)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/286
`/scratch/stefan/7769638/working/3D/286' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C2C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)NC2=CC=C1)

`REAL300000057272.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057272.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057272/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057272 none CC1=C2C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)NC2=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 7, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 15, 35, 35, 35, 35, 35, 1, 1, 1, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 20, 21, 22, 23, 24, 36, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057272 none CC1=C2C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)NC2=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 26, 26, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 26, 10, 7, 1, 1, 1, 1, 35, 35, 35, 35] 35
rigid atoms, others: [32, 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, 36, 37, 38, 39])
total number of confs: 66
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057272 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057272
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057272/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057272
Building REAL300000057273
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057273'
/scratch/stefan/7769638/working/building/REAL300000057273 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057273

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057273/0 /scratch/stefan/7769638/working/building/REAL300000057273 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 287)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/287
`/scratch/stefan/7769638/working/3D/287' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)(F)F)O2)C=C1)

`REAL300000057273.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057273.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057273/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057273 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)(F)F)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', '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, 11, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 1, 1, 7, 7, 6, 6, 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, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 10, 10, 10, 28, 28, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 8, 10, 28, 37, 37, 1, 1] 37
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 70
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057273 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)(F)F)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', '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, 11, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 1, 1, 7, 7, 6, 6, 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, 7, 3, 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, 37, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 37, 37, 37, 37, 37, 15, 7, 1, 1, 37, 37] 37
rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057273 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057273
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057273/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057273
Building REAL300000057274
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057274'
/scratch/stefan/7769638/working/building/REAL300000057274 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057274

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057274/0 /scratch/stefan/7769638/working/building/REAL300000057274 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 288)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/288
`/scratch/stefan/7769638/working/3D/288' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=CC(Cl)=C2)C=C1)

`REAL300000057274.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057274.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057274/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057274 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=CC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 28, 28, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 7, 12, 28, 51, 51, 51, 1, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057274 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=CC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 19, 18, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 18, 6, 1, 1, 1, 51, 51] 51
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, 31])
total number of confs: 137
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057274 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057274
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057274/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057274
Building REAL300000057275
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057275'
/scratch/stefan/7769638/working/building/REAL300000057275 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057275

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057275/0 /scratch/stefan/7769638/working/building/REAL300000057275 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 289)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/289
`/scratch/stefan/7769638/working/3D/289' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C(F)(F)F)SC=C2)C=C1)

`REAL300000057275.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057275.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057275/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057275 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C(F)(F)F)SC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', '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, 11, 8, 8, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 1, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 19, 19, 19, 47, 47, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 11, 19, 47, 69, 69, 1, 1] 69
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057275 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C(F)(F)F)SC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', '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, 11, 8, 8, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 1, 7, 7, 6, 6, 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, 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, 30, 9, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 69, 69, 69, 69, 69, 30, 9, 1, 1, 69, 69] 69
rigid atoms, others: [12, 13, 14, 15, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057275 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057275
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057275/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057275
Building REAL300000057276
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057276'
/scratch/stefan/7769638/working/building/REAL300000057276 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057276

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057276/0 /scratch/stefan/7769638/working/building/REAL300000057276 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 290)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/290
`/scratch/stefan/7769638/working/3D/290' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCOCC2)C=C1)

`REAL300000057276.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057276.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057276/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057276 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCOCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 12, 12, 12, 32, 32, 85, 85, 85, 85, 85, 118, 118, 118, 118, 118, 1, 1, 1, 1, 8, 12, 32, 85, 85, 118, 118, 118, 118, 118, 118, 118, 118, 118, 1, 1] 118
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 266
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057276 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCOCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 73, 75, 75, 71, 34, 33, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 75, 75, 75, 75, 71, 33, 10, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 75, 75] 106
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 229
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057276 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCOCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 58, 58, 58, 21, 21, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 58, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 106] 106
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43])
total number of confs: 301
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057276 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057276
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057276/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057276
Building REAL300000057277
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057277'
/scratch/stefan/7769638/working/building/REAL300000057277 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057277

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057277/0 /scratch/stefan/7769638/working/building/REAL300000057277 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 291)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/291
`/scratch/stefan/7769638/working/3D/291' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=CC=C3)CC2)C=C1)

`REAL300000057277.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057277.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057277/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057277 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 6, 6, 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, 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, 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, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 10, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 47, 48, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 51
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057277 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 6, 6, 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, 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, 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, 26, 27, 26, 27, 27, 26, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 27, 27, 27, 27, 26, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 27, 27] 27
rigid atoms, others: [32, 33, 34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 15, 16, 17, 46, 43, 23, 24, 45, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 47, 48])
total number of confs: 82
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057277 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 6, 6, 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, 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, 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, 9, 9, 9, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 27, 27, 27, 27, 27, 9, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 27, 27] 27
rigid atoms, others: [38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48])
total number of confs: 71
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057277 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057277
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057277/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057277
Building REAL300000057278
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057278'
/scratch/stefan/7769638/working/building/REAL300000057278 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057278

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057278/0 /scratch/stefan/7769638/working/building/REAL300000057278 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 292)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/292
`/scratch/stefan/7769638/working/3D/292' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=NNC=C32)C=C1)

`REAL300000057278.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057278.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057278/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057278 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=NNC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 30, 30, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 10, 16, 30, 45, 45, 45, 45, 45, 1, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 90
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057278 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=NNC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 4, 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, 47, 47, 23, 22, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 22, 8, 1, 1, 1, 1, 1, 47, 47] 47
rigid atoms, others: [32, 33, 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, 34, 35, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 125
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057278 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057278
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057278/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057278
Building REAL300000057279
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057279'
/scratch/stefan/7769638/working/building/REAL300000057279 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057279

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057279/0 /scratch/stefan/7769638/working/building/REAL300000057279 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 293)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/293
`/scratch/stefan/7769638/working/3D/293' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CC(F)=C1F)

`REAL300000057279.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057279.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057279/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057279 none CN(C)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CC(F)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 4, 4, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 8, 18, 18, 18, 18, 18, 1, 1] 18
rigid atoms, others: [1, 3, 4, 5, 39, 40, 20, 21, 22, 23, 24, 25] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057279 none CN(C)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CC(F)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 7, 1, 1, 1, 1, 18, 18] 18
rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057279 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057279
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057279/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057279
Building REAL300000057280
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057280'
/scratch/stefan/7769638/working/building/REAL300000057280 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057280

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057280/0 /scratch/stefan/7769638/working/building/REAL300000057280 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 294)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/294
`/scratch/stefan/7769638/working/3D/294' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(O)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl)

`REAL300000057280.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057280.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057280/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057280 none CC1=CC(O)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2, 1, 2, 9, 14, 26, 26, 26, 26, 26, 1] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 36, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 77
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057280 none CC1=CC(O)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 25, 26, 22, 22, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 26, 26, 26, 26, 26, 26, 52, 22, 11, 7, 1, 1, 1, 1, 26] 52
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 111
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057280 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057280
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057280/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057280
Building REAL300000057281
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057281'
/scratch/stefan/7769638/working/building/REAL300000057281 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057281

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057281/0 /scratch/stefan/7769638/working/building/REAL300000057281 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 295)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/295
`/scratch/stefan/7769638/working/3D/295' -> `0.mol2'
Preparing input files

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

`REAL300000057281.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057281.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057281/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057281 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(F)C=CC(F)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 15, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 15, 15, 15, 26, 26, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 8, 15, 26, 65, 65, 1, 1] 65
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 118
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057281 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(F)C=CC(F)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 15, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 74, 74, 74, 74, 30, 30, 30, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 30, 11, 1, 1, 74, 74] 74
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 195
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057281 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057281
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057281/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057281
Building REAL300000057282
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057282'
/scratch/stefan/7769638/working/building/REAL300000057282 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057282

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057282/0 /scratch/stefan/7769638/working/building/REAL300000057282 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 296)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/296
`/scratch/stefan/7769638/working/3D/296' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=C1C(F)(F)F)

`REAL300000057282.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057282.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057282/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057282 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=C1C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 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: [20, 20, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 27, 27, 20, 27, 27, 27, 27, 27, 27, 27, 20, 20, 20, 16, 7, 1, 1, 1, 1, 27, 27, 27] 27
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 102
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057282 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=C1C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 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, 3, 3, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 11, 27, 27, 27, 27, 27, 1, 1, 1] 27
rigid atoms, others: [1, 36, 37, 38, 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, 35])
total number of confs: 77
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057282 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057282
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057282/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057282
Building REAL300000057283
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057283'
/scratch/stefan/7769638/working/building/REAL300000057283 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057283

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057283/0 /scratch/stefan/7769638/working/building/REAL300000057283 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 297)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/297
`/scratch/stefan/7769638/working/3D/297' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC(F)=C(Cl)C=C32)C=C1)

`REAL300000057283.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057283.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057283/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057283 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC(F)=C(Cl)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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, 9, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 9, 14, 21, 21, 21, 21, 21, 21, 1, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 23, 24, 25, 26, 36] set([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: 47
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057283 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC(F)=C(Cl)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 21, 21] 21
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 23, 24, 25, 26, 27, 28, 36])
total number of confs: 51
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057283 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057283
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057283/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057283
Building REAL300000057284
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057284'
/scratch/stefan/7769638/working/building/REAL300000057284 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057284

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057284/0 /scratch/stefan/7769638/working/building/REAL300000057284 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 298)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/298
`/scratch/stefan/7769638/working/3D/298' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CCC1=CC=CC=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057284.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057284.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057284/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057284 none CCC(CCC1=CC=CC=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [54, 31, 7, 3, 1, 1, 1, 1, 1, 1, 1, 31, 31, 83, 83, 83, 178, 184, 184, 178, 178, 184, 184, 184, 184, 54, 54, 54, 54, 54, 7, 7, 3, 3, 1, 1, 1, 1, 1, 83, 178, 184, 184, 184, 184] 196
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44])
total number of confs: 685
number of broken/clashed sets: 103
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057284 none CCC(CCC1=CC=CC=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [76, 45, 45, 45, 149, 182, 184, 184, 183, 184, 184, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 149, 149, 182, 182, 184, 184, 184, 184, 184, 15, 7, 1, 1, 1, 1] 196
rigid atoms, others: [41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 847
number of broken/clashed sets: 103
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057284 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057284
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057284/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057284
Building REAL300000057285
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057285'
/scratch/stefan/7769638/working/building/REAL300000057285 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057285

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057285/0 /scratch/stefan/7769638/working/building/REAL300000057285 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 299)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/299
`/scratch/stefan/7769638/working/3D/299' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=C(C(CC(C)C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000057285.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057285.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057285/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057285 none CCC1=CC=C(C(CC(C)C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 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
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 11, 27, 29, 29, 11, 11, 43, 44, 44, 113, 125, 125, 125, 125, 125, 125, 125, 125, 1, 1, 4, 4, 4, 3, 3, 1, 1, 27, 27, 29, 29, 29, 29, 29, 29, 29, 43, 113, 125, 125, 125, 125, 1, 1] 131
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 49, 50, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 434
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057285 none CCC1=CC=C(C(CC(C)C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 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
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [124, 51, 51, 125, 125, 51, 51, 51, 69, 71, 71, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 125, 125, 124, 124, 124, 124, 124, 125, 125, 69, 69, 71, 71, 71, 71, 71, 71, 71, 16, 7, 1, 1, 1, 1, 125, 125] 131
rigid atoms, others: [48, 45, 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, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50])
total number of confs: 749
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057285 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057285
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057285/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057285
Building REAL300000057286
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057286'
/scratch/stefan/7769638/working/building/REAL300000057286 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057286

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057286/0 /scratch/stefan/7769638/working/building/REAL300000057286 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 300)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/300
`/scratch/stefan/7769638/working/3D/300' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057286.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057286.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057286/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057286 none CCOC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 40, 47, 47, 44, 44, 47, 47, 47, 47, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 9, 40, 47, 47, 47, 47, 1, 1, 1, 1] 62
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 41, 42, 39, 40, 21, 22, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 150
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057286 none CCOC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 47, 47, 47, 47, 47, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 62, 62, 62, 62, 62, 47, 47, 47, 47, 47, 14, 7, 1, 1, 1, 1, 47, 47, 47, 47] 62
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 107
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057286 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057286
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057286/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057286
Building REAL300000057287
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057287'
/scratch/stefan/7769638/working/building/REAL300000057287 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057287

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057287/0 /scratch/stefan/7769638/working/building/REAL300000057287 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 301)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/301
`/scratch/stefan/7769638/working/3D/301' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3CCOC3)C=C2)C=C1)

`REAL300000057287.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057287.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057287/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057287 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3CCOC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 18, 18, 18, 43, 43, 72, 72, 43, 43, 142, 201, 201, 201, 201, 72, 72, 1, 1, 1, 1, 9, 18, 43, 72, 72, 201, 201, 201, 201, 201, 201, 201, 72, 72, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 44, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 547
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057287 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3CCOC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 60, 72, 56, 72, 72, 55, 22, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 11, 32, 32, 32, 32, 1, 1, 72, 72, 72, 72, 55, 22, 7, 1, 1, 32, 32, 32, 32, 32, 32, 32, 1, 1, 72, 72] 201
rigid atoms, others: [32, 33, 41, 42, 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, 34, 35, 36, 37, 38, 39, 40, 43, 44])
total number of confs: 344
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057287 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3CCOC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 126, 126, 126, 63, 63, 19, 13, 32, 32, 7, 1, 1, 1, 1, 1, 1, 32, 32, 201, 201, 201, 201, 201, 126, 63, 32, 32, 1, 1, 1, 1, 1, 1, 1, 32, 32, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44])
total number of confs: 648
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057287 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057287
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057287/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057287
Building REAL300000057288
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057288'
/scratch/stefan/7769638/working/building/REAL300000057288 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057288

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057288/0 /scratch/stefan/7769638/working/building/REAL300000057288 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 302)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/302
`/scratch/stefan/7769638/working/3D/302' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NS1)

`REAL300000057288.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057288.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057288/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057288 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 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, 2, 2, 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: [16, 16, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 16, 23, 23, 23, 23, 16, 16, 16, 10, 7, 1, 1, 1, 1, 23, 23] 23
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 55
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057288 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [12, 1, 12, 12, 16, 17, 17, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 13, 13, 13, 16, 23, 23, 23, 23, 23, 1, 1] 23
rigid atoms, others: [1, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 61
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057288 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057288
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057288/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057288
Building REAL300000057289
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057289'
/scratch/stefan/7769638/working/building/REAL300000057289 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057289

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057289/0 /scratch/stefan/7769638/working/building/REAL300000057289 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 303)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/303
`/scratch/stefan/7769638/working/3D/303' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C=N2)C=C1)

`REAL300000057289.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057289.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057289/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057289 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 7, 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, 3, 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, 6, 8, 8, 8, 18, 18, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 6, 8, 18, 20, 20, 20, 1, 1] 20
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 44
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057289 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 13, 12, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 12, 6, 1, 1, 1, 22, 22] 22
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, 31])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057289 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057289
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057289/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057289
Building REAL300000057290
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057290'
/scratch/stefan/7769638/working/building/REAL300000057290 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057290

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057290/0 /scratch/stefan/7769638/working/building/REAL300000057290 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 304)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/304
`/scratch/stefan/7769638/working/3D/304' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057290.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057290.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057290/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057290 none CC1=NN=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 6, 20, 33, 33, 33, 33, 33] 33
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057290 none CC1=NN=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 26, 26, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 33, 33, 33, 33, 26, 10, 7, 1, 1, 1, 1] 33
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057290 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057290
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057290/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057290
Building REAL300000057291
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057291'
/scratch/stefan/7769638/working/building/REAL300000057291 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057291

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057291/0 /scratch/stefan/7769638/working/building/REAL300000057291 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 305)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/305
`/scratch/stefan/7769638/working/3D/305' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(O)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057291.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057291.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057291/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057291 none CC1(O)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 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]
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: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 6, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 1, 1, 1, 1] 60
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 39, 20, 21, 36, 26, 27, 28, 29, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35])
total number of confs: 61
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057291 none CC1(O)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 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]
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, 20, 20, 20, 20, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 60, 20, 20, 20, 20, 13, 7, 1, 1, 1, 1, 20, 20, 20, 20] 60
rigid atoms, others: [32, 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, 36, 37, 38, 39])
total number of confs: 107
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057291 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057291
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057291/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057291
Building REAL300000057292
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057292'
/scratch/stefan/7769638/working/building/REAL300000057292 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057292

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057292/0 /scratch/stefan/7769638/working/building/REAL300000057292 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 306)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/306
`/scratch/stefan/7769638/working/3D/306' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CN=C1C1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057292.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057292.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057292/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057292 none CN1C=CN=C1C1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 6, 6, 6, 6, 6, 23, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 23, 44, 44, 44, 44, 44, 6, 6] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057292 none CN1C=CN=C1C1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 22, 1, 1] 44
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 41, 24, 42, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40])
total number of confs: 63
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057292 none CN1C=CN=C1C1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 22, 22, 22, 22, 22, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 44, 44, 44, 44, 44, 22, 22, 22, 22, 22, 13, 7, 1, 1, 1, 1, 22, 22] 44
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 86
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057292 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057292
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057292/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057292
Building REAL300000057293
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057293'
/scratch/stefan/7769638/working/building/REAL300000057293 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057293

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057293/0 /scratch/stefan/7769638/working/building/REAL300000057293 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 307)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/307
`/scratch/stefan/7769638/working/3D/307' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CCC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057293.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057293.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057293/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057293 none COC1CCC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 12, 12, 35, 36, 36, 74, 78, 78, 74, 78, 78, 78, 78, 78, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 35, 74, 78, 78, 78, 78, 1, 1, 1, 1] 78
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 41, 42, 21, 22, 26, 27, 28, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 242
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057293 none COC1CCC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 29, 29, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 29, 17, 7, 1, 1, 1, 1, 78, 78, 78, 78] 78
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057293 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057293
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057293/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057293
Building REAL300000057294
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057294'
/scratch/stefan/7769638/working/building/REAL300000057294 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057294

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057294/0 /scratch/stefan/7769638/working/building/REAL300000057294 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 308)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/308
`/scratch/stefan/7769638/working/3D/308' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC(F)(F)C1)

`REAL300000057294.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057294.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057294/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057294 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC(F)(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [29, 29, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 49, 49, 49, 49, 49, 29, 29, 29, 15, 7, 1, 1, 1, 1, 49, 49, 49, 49, 49] 49
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35])
total number of confs: 123
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057294 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CC(F)(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [10, 1, 10, 10, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 10, 10, 10, 27, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1] 49
rigid atoms, others: [32, 1, 34, 35, 33, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 133
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057294 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057294
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057294/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057294
Building REAL300000057295
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057295'
/scratch/stefan/7769638/working/building/REAL300000057295 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057295

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057295/0 /scratch/stefan/7769638/working/building/REAL300000057295 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 309)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/309
`/scratch/stefan/7769638/working/3D/309' -> `0.mol2'
Preparing input files

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

`REAL300000057295.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057295.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057295/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057295 none CC(C)(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(C)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [33, 14, 33, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 37, 41, 41, 33, 33, 33, 33, 33, 33, 14, 6, 6, 1, 1, 1, 1, 41, 41, 41] 41
rigid atoms, others: [32, 33, 34, 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, 35, 36, 37])
total number of confs: 181
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057295 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057295
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057295/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057295
Building REAL300000057296
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057296'
/scratch/stefan/7769638/working/building/REAL300000057296 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057296

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057296/0 /scratch/stefan/7769638/working/building/REAL300000057296 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 310)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/310
`/scratch/stefan/7769638/working/3D/310' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(O)C=CC=C3S2)C=C1)

`REAL300000057296.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057296.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057296/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057296 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(O)C=CC=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 6, 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, 4, 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, 1, 1, 10, 13, 13, 13, 38, 38, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 10, 13, 38, 54, 108, 54, 54, 54, 1, 1] 108
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 23, 24, 25, 26, 36] set([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: 208
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057296 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(O)C=CC=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 6, 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, 4, 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, 54, 54, 54, 54, 54, 52, 22, 22, 22, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 52, 22, 9, 1, 2, 1, 1, 1, 54, 54] 108
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 31, 35, 36])
total number of confs: 147
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057296 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057296
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057296/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057296
Building REAL300000057297
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057297'
/scratch/stefan/7769638/working/building/REAL300000057297 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057297

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057297/0 /scratch/stefan/7769638/working/building/REAL300000057297 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 311)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/311
`/scratch/stefan/7769638/working/3D/311' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C3=CC=CC=C3CCC2F)C=C1)

`REAL300000057297.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057297.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057297/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057297 none O=C([O-])C1=CC=C(NC(=O)NN=C2C3=CC=CC=C3CCC2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 8, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 48
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057297 none O=C([O-])C1=CC=C(NC(=O)NN=C2C3=CC=CC=C3CCC2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 18
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 23, 24, 25, 26, 27, 28])
total number of confs: 43
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057297 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057297
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057297/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057297
Building REAL300000057298
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057298'
/scratch/stefan/7769638/working/building/REAL300000057298 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057298

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057298/0 /scratch/stefan/7769638/working/building/REAL300000057298 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 312)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/312
`/scratch/stefan/7769638/working/3D/312' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F)

`REAL300000057298.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057298.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057298/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057298 none CN(C)C1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 17, 18, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 10, 17, 33, 33, 33, 33, 33, 1] 35
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 40, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 103
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057298 none CN(C)C1=CC(F)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 33, 35, 33, 33, 33, 33, 22, 22, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 33, 33, 33, 35, 35, 35, 35, 35, 35, 33, 22, 10, 7, 1, 1, 1, 1, 33] 35
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])
total number of confs: 69
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057298 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057298
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057298/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057298
Building REAL300000057299
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057299'
/scratch/stefan/7769638/working/building/REAL300000057299 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057299

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057299/0 /scratch/stefan/7769638/working/building/REAL300000057299 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 313)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/313
`/scratch/stefan/7769638/working/3D/313' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C(C)C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057299.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057299.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057299/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057299 none COC(=O)C1=C(C)C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 21, 22, 22, 51, 60, 60, 51, 54, 60, 60, 60, 60, 1, 12, 12, 12, 2, 2, 2, 1, 7, 21, 51, 60, 60, 60, 60] 73
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 253
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057299 none COC(=O)C1=C(C)C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 60, 73, 60, 60, 60, 60, 31, 31, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 60, 73, 73, 73, 60, 60, 60, 60, 31, 10, 6, 1, 1, 1, 1] 73
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 154
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057299 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057299
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057299/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057299
Building REAL300000057300
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057300'
/scratch/stefan/7769638/working/building/REAL300000057300 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057300

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057300/0 /scratch/stefan/7769638/working/building/REAL300000057300 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 314)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/314
`/scratch/stefan/7769638/working/3D/314' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=NC=C2)C=C1)

`REAL300000057300.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057300.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057300/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057300 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=NC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 9, 15, 15, 15, 44, 44, 134, 134, 134, 134, 134, 140, 140, 140, 140, 140, 1, 1, 1, 1, 9, 15, 44, 134, 134, 140, 140, 140, 140, 1, 1] 140
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: 212
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057300 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=NC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 94, 94, 94, 94, 91, 49, 48, 49, 12, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 94, 94, 94, 94, 91, 48, 12, 1, 1, 5, 5, 5, 5, 94, 94] 98
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057300 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=NC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 98, 98, 98, 98, 96, 55, 55, 55, 21, 21, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 96, 55, 21, 5, 5, 1, 1, 1, 1, 98, 98] 98
rigid atoms, others: [33, 34, 35, 36, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 268
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057300 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057300/1 /scratch/stefan/7769638/working/building/REAL300000057300 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 315)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/315
`/scratch/stefan/7769638/working/3D/315' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=[NH+]C=C2)C=C1)

`REAL300000057300.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057300.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057300/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057300 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=[NH+]C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 4, 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, 3, 7, 7, 7, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 3, 7, 13, 15, 15, 15, 15, 15, 15, 1, 1] 15
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 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])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057300 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=[NH+]C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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: [35, 34, 35, 34, 35, 35, 32, 22, 22, 22, 10, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 2, 5, 5, 35, 35, 35, 35, 32, 22, 10, 1, 1, 5, 5, 5, 5, 35, 35] 35
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057300 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2=CC=[NH+]C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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: [35, 35, 35, 35, 35, 35, 35, 27, 27, 27, 15, 15, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 27, 15, 5, 5, 1, 1, 1, 1, 35, 35] 35
rigid atoms, others: [34, 35, 36, 37, 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, 38, 39])
total number of confs: 110
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057300 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057300
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057300/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057300/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057300
Building REAL300000057301
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057301'
/scratch/stefan/7769638/working/building/REAL300000057301 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057301

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057301/0 /scratch/stefan/7769638/working/building/REAL300000057301 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 316)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/316
`/scratch/stefan/7769638/working/3D/316' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2CCCOCC2)C=C1)

`REAL300000057301.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057301.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057301/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057301 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCCOCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 12, 12, 12, 23, 23, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 8, 12, 23, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1] 54
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 144
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057301 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCCOCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 29, 29, 29, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 29, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56] 56
rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 38, 39])
total number of confs: 157
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057301 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057301
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057301/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057301
Building REAL300000057302
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057302'
/scratch/stefan/7769638/working/building/REAL300000057302 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057302

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057302/0 /scratch/stefan/7769638/working/building/REAL300000057302 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 317)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/317
`/scratch/stefan/7769638/working/3D/317' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC[C@@H]2C[C@H]2C2=CC=CC=C2)C=C1)

`REAL300000057302.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057302.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057302/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057302 none O=C([O-])C1=CC=C(NC(=O)NN=CC[C@@H]2C[C@H]2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 11, 11, 11, 22, 22, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 9, 11, 22, 90, 90, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 612
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057302 none O=C([O-])C1=CC=C(NC(=O)NN=CC[C@@H]2C[C@H]2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 187, 101, 101, 101, 68, 68, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 201, 201, 201, 201, 187, 101, 68, 9, 9, 1, 1, 4, 4, 1, 4, 4, 201, 201] 201
rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 593
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057302 none O=C([O-])C1=CC=C(NC(=O)NN=CC[C@@H]2C[C@H]2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 199, 142, 142, 142, 117, 117, 20, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 142, 117, 20, 20, 4, 4, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42])
total number of confs: 598
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057302 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057302
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057302/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057302
Building REAL300000057303
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057303'
/scratch/stefan/7769638/working/building/REAL300000057303 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057303

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057303/0 /scratch/stefan/7769638/working/building/REAL300000057303 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 318)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/318
`/scratch/stefan/7769638/working/3D/318' -> `0.mol2'
Preparing input files

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

`REAL300000057303.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057303.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057303/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057303 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'F', 'F', '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, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [32, 32, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 69, 69, 69, 69, 88, 88, 69, 69, 32, 32, 32, 12, 7, 1, 1, 1, 1, 69, 69, 88, 69] 88
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057303 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'F', 'F', '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, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 11, 11, 38, 38, 38, 68, 69, 69, 68, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 12, 12, 1, 1, 11, 11, 11, 38, 68, 69, 69, 69, 69, 1, 1, 12, 1] 88
rigid atoms, others: [1, 34, 35, 37, 16, 17, 18, 19, 20, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 228
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057303 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057303
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057303/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057303
Building REAL300000057304
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057304'
/scratch/stefan/7769638/working/building/REAL300000057304 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057304

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057304/0 /scratch/stefan/7769638/working/building/REAL300000057304 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 319)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/319
`/scratch/stefan/7769638/working/3D/319' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2CC2C2=CC=C(F)C=C2)C=C1)

`REAL300000057304.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057304.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057304/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057304 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CC2C2=CC=C(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', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 3, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 25
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 67
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057304 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CC2C2=CC=C(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', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [169, 159, 169, 149, 169, 169, 149, 60, 59, 60, 12, 12, 1, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 169, 169, 169, 169, 149, 59, 12, 1, 1, 1, 1, 4, 4, 4, 4, 169, 169] 169
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 549
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057304 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CC2C2=CC=C(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', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [169, 169, 169, 164, 169, 169, 164, 90, 90, 90, 36, 36, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 164, 90, 36, 4, 4, 4, 4, 1, 1, 1, 1, 169, 169] 169
rigid atoms, others: [34, 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, 38, 39])
total number of confs: 498
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057304 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057304
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057304/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057304
Building REAL300000057305
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057305'
/scratch/stefan/7769638/working/building/REAL300000057305 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057305

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057305/0 /scratch/stefan/7769638/working/building/REAL300000057305 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 320)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/320
`/scratch/stefan/7769638/working/3D/320' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CCC2=CC=CC(OC(F)(F)F)=C2)C=C1)

`REAL300000057305.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057305.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057305/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057305 none O=C([O-])C1=CC=C(NC(=O)NN=CCC2=CC=CC(OC(F)(F)F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 30, 59, 59, 59, 59, 59, 201, 201, 201, 201, 59, 1, 1, 1, 1, 5, 5, 6, 30, 30, 59, 59, 59, 59, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 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])
total number of confs: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057305 none O=C([O-])C1=CC=C(NC(=O)NN=CCC2=CC=CC(OC(F)(F)F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 51, 59, 59, 51, 21, 21, 21, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 13, 15, 15, 15, 1, 59, 59, 59, 59, 51, 21, 20, 6, 6, 1, 1, 1, 1, 59, 59] 201
rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 232
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057305 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057305
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057305/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057305
Building REAL300000057306
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057306'
/scratch/stefan/7769638/working/building/REAL300000057306 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057306

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057306/0 /scratch/stefan/7769638/working/building/REAL300000057306 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 321)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/321
`/scratch/stefan/7769638/working/3D/321' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CC2CC1(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C2)

`REAL300000057306.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057306.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057306/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057306 none CC(C)(C)OC(=O)N1CC2CC1(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [8, 7, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 17, 21, 21, 17, 21, 21, 21, 21, 21, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 9, 17, 21, 21, 21, 21, 1, 1] 31
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 40, 50, 41, 39, 49, 27, 5] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 94
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057306 none CC(C)(C)OC(=O)N1CC2CC1(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 28, 21, 28, 21, 21, 21, 21, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 21, 21, 21, 21, 21, 8, 5, 5, 1, 1, 1, 1, 21, 21] 31
rigid atoms, others: [45, 46, 47, 48, 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, 38, 39, 40, 41, 42, 43, 44, 49, 50])
total number of confs: 71
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057306 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057306
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057306/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057306
Building REAL300000057307
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057307'
/scratch/stefan/7769638/working/building/REAL300000057307 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057307

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057307/0 /scratch/stefan/7769638/working/building/REAL300000057307 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 322)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/322
`/scratch/stefan/7769638/working/3D/322' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCCC1)

`REAL300000057307.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057307.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057307/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057307 none COC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [103, 94, 34, 34, 9, 9, 6, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 144, 148, 148, 148, 141, 103, 103, 103, 94, 34, 9, 6, 1, 1, 1, 1, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148] 148
rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 555
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057307 none COC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [19, 9, 1, 9, 44, 44, 75, 76, 76, 146, 148, 148, 146, 147, 148, 148, 148, 148, 1, 1, 1, 1, 1, 1, 19, 19, 19, 9, 44, 75, 146, 148, 148, 148, 148, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 148
rigid atoms, others: [2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 459
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057307 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057307
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057307/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057307
Building REAL300000057308
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057308'
/scratch/stefan/7769638/working/building/REAL300000057308 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057308

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057308/0 /scratch/stefan/7769638/working/building/REAL300000057308 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 323)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/323
`/scratch/stefan/7769638/working/3D/323' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C2CCCCN2C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057308.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057308.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057308/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057308 none COC(=O)C1=C2CCCCN2C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 30, 31, 31, 70, 80, 80, 75, 80, 80, 80, 80, 80, 1, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 70, 80, 80, 80, 80, 1] 118
rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 38, 46, 36, 27, 37, 31] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057308 none COC(=O)C1=C2CCCCN2C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 80, 118, 78, 80, 80, 80, 80, 80, 80, 29, 29, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 80, 118, 118, 118, 80, 80, 80, 80, 80, 80, 80, 80, 29, 8, 6, 1, 1, 1, 1, 80] 118
rigid atoms, others: [42, 43, 44, 45, 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, 38, 39, 40, 41, 46])
total number of confs: 285
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057308 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057308
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057308/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057308
Building REAL300000057309
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057309'
/scratch/stefan/7769638/working/building/REAL300000057309 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057309

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057309/0 /scratch/stefan/7769638/working/building/REAL300000057309 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 324)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/324
`/scratch/stefan/7769638/working/3D/324' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3N=CC=C23)C=C1)

`REAL300000057309.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057309.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057309/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057309 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3N=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 9, 16, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 9, 16, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 51
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057309 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3N=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 18, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 22, 23, 24, 25, 26, 36])
total number of confs: 43
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057309 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057309
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057309/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057309
Building REAL300000057310
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057310'
/scratch/stefan/7769638/working/building/REAL300000057310 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057310

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057310/0 /scratch/stefan/7769638/working/building/REAL300000057310 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 325)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/325
`/scratch/stefan/7769638/working/3D/325' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC1=CC=C(C(F)(F)F)C=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057310.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057310.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057310/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057310 none CCC(CC1=CC=C(C(F)(F)F)C=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 22, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 22, 22, 58, 58, 58, 127, 136, 136, 127, 132, 136, 136, 136, 136, 40, 40, 40, 40, 40, 5, 5, 1, 1, 1, 1, 58, 127, 136, 136, 136, 136] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 12, 13, 3, 36, 38, 37] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44])
total number of confs: 564
number of broken/clashed sets: 131
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057310 none CCC(CC1=CC=C(C(F)(F)F)C=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 39, 39, 39, 112, 136, 136, 115, 135, 136, 136, 136, 136, 136, 19, 19, 7, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 112, 112, 136, 136, 136, 136, 19, 7, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 631
number of broken/clashed sets: 131
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057310 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057310
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057310/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057310
Building REAL300000057311
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057311'
/scratch/stefan/7769638/working/building/REAL300000057311 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057311

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057311/0 /scratch/stefan/7769638/working/building/REAL300000057311 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 326)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/326
`/scratch/stefan/7769638/working/3D/326' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C(F)=C2F)C=C1)

`REAL300000057311.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057311.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057311/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057311 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C(F)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 7, 7, 6, 6, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 9, 9, 9, 22, 22, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 7, 9, 22, 27, 27, 1, 1] 27
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057311 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C(F)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 7, 7, 6, 6, 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, 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, 15, 15, 15, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 15, 10, 1, 1, 29, 29] 29
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057311 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057311
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057311/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057311
Building REAL300000057312
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057312'
/scratch/stefan/7769638/working/building/REAL300000057312 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057312

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057312/0 /scratch/stefan/7769638/working/building/REAL300000057312 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 327)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/327
`/scratch/stefan/7769638/working/3D/327' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C(F)(F)F)=C1)

`REAL300000057312.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057312.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057312/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057312 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C(F)(F)F)=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 6, 6, 24, 25, 25, 52, 59, 59, 52, 56, 59, 59, 59, 59, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 1, 6, 24, 52, 59, 59, 59, 59, 1, 1] 59
rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 20, 21, 22, 26, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 209
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057312 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C(F)(F)F)=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 59, 34, 34, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 34, 12, 7, 1, 1, 1, 1, 59, 59] 59
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, 38, 39])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057312 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057312
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057312/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057312
Building REAL300000057313
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057313'
/scratch/stefan/7769638/working/building/REAL300000057313 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057313

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057313/0 /scratch/stefan/7769638/working/building/REAL300000057313 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 328)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/328
`/scratch/stefan/7769638/working/3D/328' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC1CC1)

`REAL300000057313.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057313.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057313/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057313 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC1CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 41, 57, 57, 41, 47, 57, 57, 57, 57, 1, 1, 1, 10, 38, 38, 3, 3, 3, 1, 1, 9, 21, 41, 57, 57, 57, 57, 1, 38, 38, 38, 38, 38] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 21, 22, 23, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 321
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057313 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC1CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [114, 57, 57, 57, 57, 16, 16, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 178, 201, 201, 114, 114, 114, 57, 57, 16, 8, 6, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44])
total number of confs: 440
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057313 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC1CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 38, 38, 38, 38, 38, 38, 119, 119, 147, 147, 147, 192, 201, 201, 192, 197, 201, 201, 201, 201, 38, 9, 1, 1, 1, 1, 65, 65, 65, 38, 38, 119, 147, 192, 201, 201, 201, 201, 38, 1, 1, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 43, 44, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 651
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057313 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057313
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057313/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057313
Building REAL300000057314
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057314'
/scratch/stefan/7769638/working/building/REAL300000057314 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057314

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057314/0 /scratch/stefan/7769638/working/building/REAL300000057314 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 329)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/329
`/scratch/stefan/7769638/working/3D/329' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CC=C2CCCCC2=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057314.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057314.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057314/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057314 none CC(CC1=CC=C2CCCCC2=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 33, 33, 33, 85, 85, 85, 85, 85, 85, 85, 85, 85, 18, 18, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 85, 85, 85, 85, 85] 85
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 43, 44, 45, 46, 47, 48])
total number of confs: 248
number of broken/clashed sets: 80
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057314 none CC(CC1=CC=C2CCCCC2=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 44, 85, 85, 85, 85, 85, 85, 85, 85, 85, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 14, 14, 14, 44, 44, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 5, 3, 1, 1, 1, 1] 85
rigid atoms, others: [45, 46, 47, 48, 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, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 225
number of broken/clashed sets: 80
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057314 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057314
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057314/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057314
Building REAL300000057315
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057315'
/scratch/stefan/7769638/working/building/REAL300000057315 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057315

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057315/0 /scratch/stefan/7769638/working/building/REAL300000057315 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 330)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/330
`/scratch/stefan/7769638/working/3D/330' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057315.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057315.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057315/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057315 none CC1(C)CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 1, 1, 1, 1] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 41, 42, 7, 44, 34, 43, 21, 22, 33, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40])
total number of confs: 53
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057315 none CC1(C)CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 7, 1, 1, 1, 1, 16, 16, 16, 16] 16
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44])
total number of confs: 38
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057315 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057315
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057315/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057315
Building REAL300000057316
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057316'
/scratch/stefan/7769638/working/building/REAL300000057316 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057316

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057316/0 /scratch/stefan/7769638/working/building/REAL300000057316 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 331)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/331
`/scratch/stefan/7769638/working/3D/331' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC(C3)C2)C=C1)

`REAL300000057316.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057316.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057316/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057316 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC(C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 16, 16, 16, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 8, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1] 26
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 66
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057316 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC(C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 26
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 20, 21, 22, 23, 24, 25, 38])
total number of confs: 65
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057316 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057316
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057316/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057316
Building REAL300000057317
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057317'
/scratch/stefan/7769638/working/building/REAL300000057317 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057317

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057317/0 /scratch/stefan/7769638/working/building/REAL300000057317 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 332)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/332
`/scratch/stefan/7769638/working/3D/332' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057317.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057317.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057317/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057317 none CCCN1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 32, 33, 33, 87, 100, 100, 91, 91, 100, 100, 100, 100, 12, 12, 12, 11, 11, 5, 5, 1, 1, 10, 32, 87, 100, 100, 100, 100] 161
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 384
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057317 none CCCN1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [161, 159, 100, 100, 100, 100, 100, 39, 39, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 161, 161, 161, 161, 161, 159, 159, 100, 100, 39, 16, 7, 1, 1, 1, 1] 161
rigid atoms, others: [35, 36, 37, 38, 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])
total number of confs: 477
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057317 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057317
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057317/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057317
Building REAL300000057318
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057318'
/scratch/stefan/7769638/working/building/REAL300000057318 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057318

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057318/0 /scratch/stefan/7769638/working/building/REAL300000057318 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 333)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/333
`/scratch/stefan/7769638/working/3D/333' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=NC=CC=C23)C=C1)

`REAL300000057318.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057318.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057318/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057318 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=NC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 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, 8, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 8, 11, 17, 17, 17, 17, 17, 17, 17, 1, 1] 17
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: 44
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057318 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=NC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 17, 17] 17
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 22, 23, 24, 25, 26, 27, 36])
total number of confs: 41
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057318 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057318
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057318/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057318
Building REAL300000057319
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057319'
/scratch/stefan/7769638/working/building/REAL300000057319 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057319

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057319/0 /scratch/stefan/7769638/working/building/REAL300000057319 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 334)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/334
`/scratch/stefan/7769638/working/3D/334' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCCC2=N1)

`REAL300000057319.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057319.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057319/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057319 none CC1=CC(C)=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCCC2=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 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, 8, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 39, 44, 43, 40, 21, 22, 23, 24, 25, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 51
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057319 none CC1=CC(C)=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCCC2=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 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, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 7, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 15
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44])
total number of confs: 36
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057319 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057319
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057319/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057319
Building REAL300000057320
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057320'
/scratch/stefan/7769638/working/building/REAL300000057320 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057320

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057320/0 /scratch/stefan/7769638/working/building/REAL300000057320 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 335)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/335
`/scratch/stefan/7769638/working/3D/335' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Br)C=C2O)C=C1)

`REAL300000057320.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057320.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057320/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057320 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Br)C=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 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, 4, 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: [2, 1, 2, 1, 1, 1, 1, 1, 6, 8, 8, 8, 18, 18, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 6, 8, 18, 22, 22, 22, 44, 1, 1] 44
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 88
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057320 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Br)C=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 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, 4, 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, 22, 22, 22, 10, 10, 10, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 10, 8, 1, 1, 1, 2, 22, 22] 44
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 59
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057320 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057320
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057320/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057320
Building REAL300000057321
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057321'
/scratch/stefan/7769638/working/building/REAL300000057321 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057321

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057321/0 /scratch/stefan/7769638/working/building/REAL300000057321 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 336)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/336
`/scratch/stefan/7769638/working/3D/336' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(F)(F)F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057321.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057321.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057321/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057321 none CN1N=C(C(F)(F)F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 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, 2, 2, 2, 1, 1, 1, 8, 8, 21, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 2, 2, 2, 1, 8, 21, 36, 36, 36, 36, 36] 36
rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 28] set([5, 6, 7, 11, 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: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057321 none CN1N=C(C(F)(F)F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 23, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 36, 36, 36, 23, 11, 7, 1, 1, 1, 1] 36
rigid atoms, others: [32, 33, 34, 35, 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])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057321 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057321
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057321/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057321
Building REAL300000057322
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057322'
/scratch/stefan/7769638/working/building/REAL300000057322 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057322

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057322/0 /scratch/stefan/7769638/working/building/REAL300000057322 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 337)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/337
`/scratch/stefan/7769638/working/3D/337' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C3CCCN23)C=C1)

`REAL300000057322.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057322.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057322/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057322 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C3CCCN23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 1, 8, 10, 10, 10, 22, 22, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 8, 10, 22, 31, 31, 31, 31, 31, 31, 31, 1, 1] 31
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057322 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C3CCCN23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 21, 20, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 20, 6, 1, 1, 1, 1, 1, 1, 1, 33, 33] 33
rigid atoms, others: [32, 33, 34, 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, 11, 35, 21, 22, 23, 24, 25, 26, 27, 36])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057322 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057322
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057322/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057322
Building REAL300000057323
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057323'
/scratch/stefan/7769638/working/building/REAL300000057323 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057323

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057323/0 /scratch/stefan/7769638/working/building/REAL300000057323 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 338)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/338
`/scratch/stefan/7769638/working/3D/338' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057323.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057323.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057323/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057323 none CCC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 54, 54, 43, 44, 54, 54, 54, 54, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 43, 54, 54, 54, 54, 1, 1, 1, 1] 54
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 41, 42, 7, 44, 34, 43, 21, 22, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40])
total number of confs: 205
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057323 none CCC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 18, 7, 1, 1, 1, 1, 54, 54, 54, 54] 54
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44])
total number of confs: 103
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057323 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057323
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057323/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057323
Building REAL300000057324
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057324'
/scratch/stefan/7769638/working/building/REAL300000057324 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057324

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057324/0 /scratch/stefan/7769638/working/building/REAL300000057324 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 339)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/339
`/scratch/stefan/7769638/working/3D/339' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)OC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000057324.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057324.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057324/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057324 none COCC(C)OC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [107, 67, 20, 6, 20, 1, 1, 1, 1, 1, 1, 6, 6, 12, 13, 13, 27, 30, 30, 29, 30, 30, 30, 30, 30, 1, 1, 107, 107, 107, 67, 67, 20, 20, 20, 20, 1, 1, 6, 12, 27, 30, 30, 30, 30, 1, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 45, 46, 25, 26, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 413
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057324 none COCC(C)OC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 199, 141, 61, 141, 10, 10, 30, 30, 10, 10, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 201, 201, 201, 199, 199, 141, 141, 141, 141, 30, 30, 10, 6, 6, 1, 1, 1, 1, 30, 30] 201
rigid atoms, others: [41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46])
total number of confs: 810
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057324 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057324
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057324/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057324
Building REAL300000057325
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057325'
/scratch/stefan/7769638/working/building/REAL300000057325 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057325

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057325/0 /scratch/stefan/7769638/working/building/REAL300000057325 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 340)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/340
`/scratch/stefan/7769638/working/3D/340' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057325.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057325.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057325/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057325 none CCCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [11, 7, 1, 1, 1, 1, 1, 1, 8, 8, 34, 35, 35, 73, 83, 83, 79, 83, 83, 83, 83, 83, 1, 12, 12, 12, 11, 12, 7, 7, 1, 1, 8, 34, 73, 83, 83, 83, 83] 150
rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057325 none CCCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 83, 83, 83, 83, 42, 42, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 83, 150, 150, 150, 150, 150, 150, 150, 83, 83, 42, 16, 7, 1, 1, 1, 1] 150
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 456
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057325 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057325
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057325/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057325
Building REAL300000057326
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057326'
/scratch/stefan/7769638/working/building/REAL300000057326 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057326

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057326/0 /scratch/stefan/7769638/working/building/REAL300000057326 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 341)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/341
`/scratch/stefan/7769638/working/3D/341' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C2C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)NC2=C1)

`REAL300000057326.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057326.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057326/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057326 none CC1=CC=C2C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)NC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 15, 33, 33, 33, 33, 33, 1, 1] 33
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24, 38, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057326 none CC1=CC=C2C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)NC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 24, 24, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 24, 8, 5, 1, 1, 1, 1, 33, 33] 33
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, 38, 39])
total number of confs: 62
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057326 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057326
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057326/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057326
Building REAL300000057327
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057327'
/scratch/stefan/7769638/working/building/REAL300000057327 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057327

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057327/0 /scratch/stefan/7769638/working/building/REAL300000057327 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 342)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/342
`/scratch/stefan/7769638/working/3D/342' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CN=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057327.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057327.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057327/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057327 none CCOC1=CN=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 38, 39, 39, 83, 97, 97, 89, 90, 97, 97, 97, 97, 1, 16, 16, 16, 16, 16, 1, 1, 11, 38, 83, 97, 97, 97, 97, 1] 143
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 38, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 350
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057327 none CCOC1=CN=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [143, 142, 97, 97, 97, 97, 97, 40, 40, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 97, 143, 143, 143, 143, 143, 97, 97, 40, 15, 7, 1, 1, 1, 1, 97] 143
rigid atoms, others: [34, 35, 36, 37, 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, 38])
total number of confs: 246
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057327 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057327
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057327/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057327
Building REAL300000057328
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057328'
/scratch/stefan/7769638/working/building/REAL300000057328 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057328

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057328/0 /scratch/stefan/7769638/working/building/REAL300000057328 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 343)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/343
`/scratch/stefan/7769638/working/3D/343' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CN1C=NC=N1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057328.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057328.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057328/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057328 none CC(CN1C=NC=N1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 5, 8, 1, 8, 1, 8, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [39, 9, 1, 1, 1, 1, 1, 1, 39, 39, 105, 105, 105, 145, 151, 151, 145, 145, 151, 151, 151, 151, 39, 39, 39, 9, 9, 1, 1, 105, 145, 151, 151, 151, 151] 151
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 510
number of broken/clashed sets: 97
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057328 none CC(CN1C=NC=N1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 5, 8, 1, 8, 1, 8, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 111, 151, 151, 151, 151, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 33, 33, 33, 111, 111, 151, 151, 10, 7, 1, 1, 1, 1] 151
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 441
number of broken/clashed sets: 97
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057328 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057328
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057328/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057328
Building REAL300000057329
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057329'
/scratch/stefan/7769638/working/building/REAL300000057329 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057329

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057329/0 /scratch/stefan/7769638/working/building/REAL300000057329 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 344)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/344
`/scratch/stefan/7769638/working/3D/344' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2COC(C3CC3)C2)C=C1)

`REAL300000057329.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057329.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057329/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057329 none O=C([O-])C1=CC=C(NC(=O)NN=C2COC(C3CC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 15, 15, 15, 27, 27, 27, 27, 27, 48, 48, 27, 1, 1, 1, 1, 8, 15, 27, 27, 27, 48, 48, 48, 48, 48, 27, 27, 1, 1] 48
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 36, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 147
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057329 none O=C([O-])C1=CC=C(NC(=O)NN=C2COC(C3CC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 25, 26, 26, 25, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 26, 26, 26, 26, 25, 7, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 26, 26] 46
rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 16, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 84
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057329 none O=C([O-])C1=CC=C(NC(=O)NN=C2COC(C3CC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 20, 20, 20, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 46, 46, 46, 46, 46, 20, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 46, 46] 46
rigid atoms, others: [32, 33, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 117
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057329 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057329
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057329/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057329
Building REAL300000057330
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057330'
/scratch/stefan/7769638/working/building/REAL300000057330 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057330

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057330/0 /scratch/stefan/7769638/working/building/REAL300000057330 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 345)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/345
`/scratch/stefan/7769638/working/3D/345' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CS3)C=C2)C=C1)

`REAL300000057330.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057330.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057330/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057330 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CS3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 8, 12, 12, 12, 31, 31, 31, 31, 31, 31, 77, 77, 77, 77, 31, 31, 1, 1, 1, 1, 8, 12, 31, 31, 31, 77, 77, 77, 31, 31, 1, 1] 77
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 130
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057330 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CS3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 12, 11, 12, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 30, 30, 30, 30, 30, 11, 3, 1, 1, 11, 11, 11, 1, 1, 30, 30] 78
rigid atoms, others: [32, 36, 37, 12, 13, 14, 15, 16, 17, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39])
total number of confs: 90
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057330 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CS3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 78, 78, 78, 78, 46, 44, 46, 13, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 78, 78, 78, 78, 78, 44, 12, 11, 11, 1, 1, 1, 11, 11, 78, 78] 78
rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 240
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057330 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057330
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057330/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057330
Building REAL300000057331
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057331'
/scratch/stefan/7769638/working/building/REAL300000057331 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057331

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057331/0 /scratch/stefan/7769638/working/building/REAL300000057331 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 346)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/346
`/scratch/stefan/7769638/working/3D/346' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CCC2=CC=CC=C2)C=C1)

`REAL300000057331.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057331.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057331/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057331 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CCC2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 8, 8, 8, 32, 32, 89, 89, 89, 89, 89, 173, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 6, 8, 32, 89, 89, 173, 173, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 685
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057331 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CCC2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [91, 79, 91, 67, 91, 91, 67, 31, 30, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 11, 15, 15, 12, 15, 15, 91, 91, 91, 91, 67, 30, 6, 1, 1, 5, 5, 11, 11, 15, 15, 15, 15, 15, 91, 91] 201
rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057331 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CCC2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 198, 201, 201, 198, 108, 107, 108, 56, 56, 15, 15, 15, 15, 15, 5, 3, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 198, 107, 56, 15, 15, 5, 5, 3, 3, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45])
total number of confs: 627
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057331 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057331
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057331/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057331
Building REAL300000057332
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057332'
/scratch/stefan/7769638/working/building/REAL300000057332 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057332

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057332/0 /scratch/stefan/7769638/working/building/REAL300000057332 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 347)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/347
`/scratch/stefan/7769638/working/3D/347' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC=CC=C21)

`REAL300000057332.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057332.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057332/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057332 none CC(=O)N1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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, 11, 8, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 1, 1, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 1, 1, 1, 1] 27
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 8, 41, 42, 7, 43, 40, 21, 22, 23, 24, 25, 26, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 71
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057332 none CC(=O)N1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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, 11, 8, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 25, 27, 25, 25, 25, 25, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 25, 25, 25, 25, 25, 27, 27, 27, 25, 25, 25, 25, 13, 7, 1, 1, 1, 1, 25, 25, 25, 25] 27
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43])
total number of confs: 65
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057332 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057332
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057332/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057332
Building REAL300000057333
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057333'
/scratch/stefan/7769638/working/building/REAL300000057333 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057333

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057333/0 /scratch/stefan/7769638/working/building/REAL300000057333 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 348)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/348
`/scratch/stefan/7769638/working/3D/348' -> `0.mol2'
Preparing input files

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

`REAL300000057333.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057333.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057333/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057333 none CC(C)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 97, 97, 97, 97, 97, 97, 97, 97, 97, 1, 5, 5, 5, 4, 5, 5, 5, 1, 1, 1, 11, 39, 97, 97, 97, 97, 97, 1] 105
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 41, 23, 33, 31] set([0, 2, 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])
total number of confs: 279
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057333 none CC(C)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 97, 105, 97, 39, 97, 97, 38, 38, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 105, 105, 105, 105, 105, 105, 105, 63, 97, 97, 38, 16, 7, 1, 1, 1, 1, 97] 105
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 344
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057333 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057333
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057333/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057333
Building REAL300000057334
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057334'
/scratch/stefan/7769638/working/building/REAL300000057334 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057334

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057334/0 /scratch/stefan/7769638/working/building/REAL300000057334 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 349)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/349
`/scratch/stefan/7769638/working/3D/349' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC2C2=CC=CC=C2Cl)C=C1)

`REAL300000057334.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057334.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057334/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057334 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC2C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 10, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 10, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 54
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057334 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC2C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 32, 32, 32, 32, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 32, 32] 32
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45])
total number of confs: 88
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057334 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC2C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 32, 32] 32
rigid atoms, others: [40, 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, 44, 45])
total number of confs: 85
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057334 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057334
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057334/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057334
Building REAL300000057335
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057335'
/scratch/stefan/7769638/working/building/REAL300000057335 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057335

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057335/0 /scratch/stefan/7769638/working/building/REAL300000057335 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 350)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/350
`/scratch/stefan/7769638/working/3D/350' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=N1)

`REAL300000057335.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057335.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057335/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057335 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 18, 19, 19, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 2, 2, 2, 1, 8, 18, 41, 41, 41, 41, 41] 41
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057335 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 30, 30, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 30, 10, 7, 1, 1, 1, 1] 41
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 74
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057335 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057335
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057335/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057335
Building REAL300000057336
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057336'
/scratch/stefan/7769638/working/building/REAL300000057336 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057336

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057336/0 /scratch/stefan/7769638/working/building/REAL300000057336 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 351)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/351
`/scratch/stefan/7769638/working/3D/351' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(F)=C2OCC(F)(F)F)C=C1)

`REAL300000057336.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057336.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057336/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057336 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(F)=C2OCC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 15, 15, 38, 38, 94, 94, 94, 94, 94, 94, 94, 128, 201, 201, 201, 201, 1, 1, 1, 1, 8, 15, 38, 94, 94, 94, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057336 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(F)=C2OCC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 80, 77, 80, 80, 71, 26, 26, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 14, 14, 14, 14, 80, 80, 80, 80, 71, 26, 8, 1, 1, 1, 14, 14, 80, 80] 169
rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 252
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057336 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057336
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057336/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057336
Building REAL300000057337
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057337'
/scratch/stefan/7769638/working/building/REAL300000057337 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057337

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057337/0 /scratch/stefan/7769638/working/building/REAL300000057337 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 352)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/352
`/scratch/stefan/7769638/working/3D/352' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=C1)

`REAL300000057337.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057337/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057337 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 38, 38, 38, 97, 111, 111, 103, 108, 111, 111, 111, 111, 1, 1, 1, 1, 9, 9, 9, 9, 2, 2, 2, 1, 10, 37, 97, 111, 111, 111, 111, 2, 2, 2, 9, 9] 142
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 349
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057337 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 45, 45, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 111, 111, 111, 111, 142, 142, 142, 142, 111, 111, 111, 111, 45, 15, 7, 1, 1, 1, 1, 111, 111, 111, 142, 142] 142
rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42])
total number of confs: 237
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057337 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 46, 46, 100, 100, 100, 142, 142, 142, 142, 142, 142, 142, 142, 142, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 46, 100, 142, 142, 142, 142, 142, 9, 9, 9, 1, 1] 142
rigid atoms, others: [41, 42, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 408
number of broken/clashed sets: 32
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057337 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057337
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057337/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057337
Building REAL300000057338
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057338'
/scratch/stefan/7769638/working/building/REAL300000057338 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057338

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057338/0 /scratch/stefan/7769638/working/building/REAL300000057338 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 353)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/353
`/scratch/stefan/7769638/working/3D/353' -> `0.mol2'
Preparing input files

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

`REAL300000057338.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057338.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057338/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057338 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(O)C=CC=C2OC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.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, 11, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 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
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, 10, 17, 17, 17, 38, 38, 125, 125, 125, 44, 125, 125, 125, 201, 201, 201, 201, 1, 1, 1, 1, 10, 17, 38, 250, 125, 53, 125, 1, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 26, 27, 28, 37, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 736
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057338 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(O)C=CC=C2OC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.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, 11, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 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
376  conformations in input
total number of sets (complete confs): 376
using faster count positions algorithm for large data
unique positions, atoms: [119, 100, 119, 100, 119, 119, 88, 41, 41, 41, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 119, 119, 119, 119, 88, 41, 13, 2, 1, 1, 1, 119, 119] 376
rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 494
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057338 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057338
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057338/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057338
Building REAL300000057339
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057339'
/scratch/stefan/7769638/working/building/REAL300000057339 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057339

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057339/0 /scratch/stefan/7769638/working/building/REAL300000057339 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 354)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/354
`/scratch/stefan/7769638/working/3D/354' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2CC2(Cl)Cl)C=C1)

`REAL300000057339.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057339.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057339/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057339 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CC2(Cl)Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'Cl', '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, 11, 8, 8, 1, 5, 5, 5, 16, 16, 1, 1, 7, 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, 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, 8, 13, 13, 13, 30, 30, 52, 52, 52, 52, 1, 1, 1, 1, 8, 13, 30, 52, 52, 52, 1, 1] 52
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27])
total number of confs: 135
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057339 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CC2(Cl)Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'Cl', '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, 11, 8, 8, 1, 5, 5, 5, 16, 16, 1, 1, 7, 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, 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, 31, 31, 31, 10, 10, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 31, 10, 1, 1, 1, 55, 55] 55
rigid atoms, others: [12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 28, 29])
total number of confs: 149
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057339 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057339
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057339/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057339
Building REAL300000057340
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057340'
/scratch/stefan/7769638/working/building/REAL300000057340 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057340

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057340/0 /scratch/stefan/7769638/working/building/REAL300000057340 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 355)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/355
`/scratch/stefan/7769638/working/3D/355' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(F)(F)F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057340.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057340.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057340/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057340 none CN1N=CC(C(F)(F)F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 8, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 12, 12, 27, 27, 27, 56, 57, 57, 56, 57, 57, 57, 57, 57, 2, 2, 2, 1, 12, 26, 56, 57, 57, 57, 57] 57
rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 28] set([6, 7, 8, 11, 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: 171
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057340 none CN1N=CC(C(F)(F)F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 8, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 57, 57, 57, 57, 57, 57, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 34, 16, 7, 1, 1, 1, 1] 57
rigid atoms, others: [32, 33, 34, 35, 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])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057340 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057340
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057340/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057340
Building REAL300000057341
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057341'
/scratch/stefan/7769638/working/building/REAL300000057341 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057341

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057341/0 /scratch/stefan/7769638/working/building/REAL300000057341 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 356)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/356
`/scratch/stefan/7769638/working/3D/356' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C2CC2)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057341.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057341.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057341/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057341 none CN1N=CC(C2CC2)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 9, 9, 1, 1, 9, 9, 21, 21, 21, 54, 59, 59, 57, 57, 59, 59, 59, 59, 2, 2, 2, 1, 9, 9, 9, 9, 9, 9, 20, 54, 59, 59, 59, 59] 80
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, 37, 38, 39])
total number of confs: 192
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057341 none CN1N=CC(C2CC2)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 1, 1, 1, 1, 9, 9, 27, 27, 49, 49, 49, 79, 80, 80, 80, 80, 80, 80, 80, 80, 9, 9, 9, 9, 1, 1, 1, 1, 1, 27, 49, 79, 80, 80, 80, 80] 80
rigid atoms, others: [32, 4, 5, 6, 7, 28, 29, 30, 31] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 216
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057341 none CN1N=CC(C2CC2)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 59, 59, 59, 80, 80, 36, 36, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 80, 80, 80, 80, 80, 36, 15, 7, 1, 1, 1, 1] 80
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 181
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057341 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057341
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057341/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057341
Building REAL300000057342
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057342'
/scratch/stefan/7769638/working/building/REAL300000057342 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057342

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057342/0 /scratch/stefan/7769638/working/building/REAL300000057342 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 357)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/357
`/scratch/stefan/7769638/working/3D/357' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C2CCC2)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057342.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057342.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057342/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057342 none CN1N=CC(C2CCC2)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 1, 1, 12, 12, 36, 36, 36, 77, 88, 88, 77, 77, 88, 88, 88, 88, 2, 2, 2, 1, 9, 9, 9, 9, 9, 9, 9, 12, 35, 77, 88, 88, 88, 88] 129
rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 28] set([6, 7, 8, 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: 326
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057342 none CN1N=CC(C2CCC2)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 1, 1, 1, 1, 1, 9, 9, 36, 36, 77, 77, 77, 127, 129, 129, 127, 127, 129, 129, 129, 129, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 36, 77, 127, 129, 129, 129, 129] 129
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 366
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057342 none CN1N=CC(C2CCC2)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 88, 88, 129, 129, 129, 36, 36, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 88, 88, 88, 88, 129, 129, 129, 129, 129, 129, 129, 36, 15, 7, 1, 1, 1, 1] 129
rigid atoms, others: [39, 40, 41, 42, 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, 36, 37, 38])
total number of confs: 299
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057342 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057342
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057342/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057342
Building REAL300000057343
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057343'
/scratch/stefan/7769638/working/building/REAL300000057343 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057343

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057343/0 /scratch/stefan/7769638/working/building/REAL300000057343 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 358)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/358
`/scratch/stefan/7769638/working/3D/358' -> `0.mol2'
Preparing input files

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

`REAL300000057343.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057343.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057343/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057343 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(OC)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'O.3', 'C.3', '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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 7, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [41, 23, 23, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 23, 28, 28, 28, 28, 28, 28, 28, 41, 41, 41, 41, 41, 12, 7, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28] 47
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 169
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057343 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(OC)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'O.3', 'C.3', '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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 7, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 5, 1, 5, 5, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 2, 1, 11, 11, 11, 11, 11, 16, 28, 28, 28, 28, 28, 1, 1, 1, 2, 2, 2] 47
rigid atoms, others: [2, 36, 37, 38, 17, 18, 19, 20, 21, 22, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41])
total number of confs: 108
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057343 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057343
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057343/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057343
Building REAL300000057344
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057344'
/scratch/stefan/7769638/working/building/REAL300000057344 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057344

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057344/0 /scratch/stefan/7769638/working/building/REAL300000057344 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 359)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/359
`/scratch/stefan/7769638/working/3D/359' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC=C(O)C=C32)C=C1)

`REAL300000057344.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057344.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057344/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057344 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC=C(O)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 8, 18, 19, 19, 19, 38, 19, 1, 1] 38
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: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057344 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC=C(O)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 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, 19, 19, 19, 5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 4, 1, 1, 1, 2, 1, 19, 19] 38
rigid atoms, others: [33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 32, 23, 24, 25, 26, 27, 28])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057344 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057344
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057344/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057344
Building REAL300000057345
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057345'
/scratch/stefan/7769638/working/building/REAL300000057345 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057345

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057345/0 /scratch/stefan/7769638/working/building/REAL300000057345 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 360)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/360
`/scratch/stefan/7769638/working/3D/360' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2CC[NH+](CC3=CC=CC=C3)CC2)C=C1)

`REAL300000057345.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057345.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057345/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057345 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CC[NH+](CC3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 19, 19, 1, 1, 1, 1, 3, 5, 5, 19, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 29, 19, 19, 19, 19, 1, 1] 29
rigid atoms, others: [1, 3, 4, 5, 6, 7, 50, 51, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057345 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CC[NH+](CC3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 19, 19, 19, 19, 19, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 19, 19] 29
rigid atoms, others: [48, 34, 35, 36, 37, 38, 49, 12, 13, 14, 15, 16, 17, 18, 46, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 50, 51])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057345 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CC[NH+](CC3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 13, 13, 13, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 29, 29, 29, 29, 29, 13, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 29, 29] 29
rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50, 51])
total number of confs: 83
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057345 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057345
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057345/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057345
Building REAL300000057346
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057346'
/scratch/stefan/7769638/working/building/REAL300000057346 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057346

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057346/0 /scratch/stefan/7769638/working/building/REAL300000057346 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 361)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/361
`/scratch/stefan/7769638/working/3D/361' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(C)(C)C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057346.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057346.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057346/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057346 none C[NH+](C)CC(C)(C)C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 28, 41, 41, 28, 8, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 28, 8, 7, 1, 1, 1, 1] 41
rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 122
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057346 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057346
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057346/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057346
Building REAL300000057347
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057347'
/scratch/stefan/7769638/working/building/REAL300000057347 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057347

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057347/0 /scratch/stefan/7769638/working/building/REAL300000057347 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 362)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/362
`/scratch/stefan/7769638/working/3D/362' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2CCC3CC3C2)C=C1)

`REAL300000057347.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057347.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057347/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057347 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCC3CC3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 12, 12, 12, 21, 21, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 9, 12, 21, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1] 57
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 141
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057347 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCC3CC3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 26, 27, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 26, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58] 58
rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 38, 39])
total number of confs: 157
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057347 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057347
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057347/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057347
Building REAL300000057348
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057348'
/scratch/stefan/7769638/working/building/REAL300000057348 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057348

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057348/0 /scratch/stefan/7769638/working/building/REAL300000057348 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 363)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/363
`/scratch/stefan/7769638/working/3D/363' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C2OCCCC2=C1)

`REAL300000057348.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057348.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057348/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057348 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C2OCCCC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 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, 4, 7, 6, 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, 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: [30, 30, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 68, 68, 68, 68, 68, 68, 68, 68, 68, 30, 30, 30, 16, 7, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 68, 68] 68
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 123
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057348 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C2OCCCC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 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, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 40, 41, 41, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 40, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 1] 68
rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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])
total number of confs: 191
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057348 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057348
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057348/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057348
Building REAL300000057349
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057349'
/scratch/stefan/7769638/working/building/REAL300000057349 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057349

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057349/0 /scratch/stefan/7769638/working/building/REAL300000057349 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 364)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/364
`/scratch/stefan/7769638/working/3D/364' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2CCSCC2)C=C1)

`REAL300000057349.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057349.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057349/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057349 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCSCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 14, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 11, 11, 11, 20, 20, 43, 43, 43, 43, 43, 1, 1, 1, 1, 9, 11, 20, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 36, 35] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057349 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCSCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 14, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 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, 47, 47, 24, 23, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 23, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47] 47
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 36, 35])
total number of confs: 131
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057349 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057349
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057349/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057349
Building REAL300000057350
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057350'
/scratch/stefan/7769638/working/building/REAL300000057350 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057350

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057350/0 /scratch/stefan/7769638/working/building/REAL300000057350 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 365)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/365
`/scratch/stefan/7769638/working/3D/365' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN=C1Br)

`REAL300000057350.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057350.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057350/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057350 none CN1C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 17, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 7, 7, 19, 20, 20, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 2, 2, 2, 7, 19, 54, 54, 54, 54, 54, 1] 54
rigid atoms, others: [0, 1, 2, 3, 32, 18, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057350 none CN1C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 17, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 34, 34, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 34, 12, 7, 1, 1, 1, 1, 54] 54
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057350 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057350
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057350/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057350
Building REAL300000057351
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057351'
/scratch/stefan/7769638/working/building/REAL300000057351 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057351

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057351/0 /scratch/stefan/7769638/working/building/REAL300000057351 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 366)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/366
`/scratch/stefan/7769638/working/3D/366' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)NC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057351.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057351.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057351/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057351 none CCOC(=O)NC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 25, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 52, 52, 44, 44, 52, 52, 52, 52, 1, 1, 55, 55, 55, 55, 55, 7, 1, 1, 1, 1, 1, 9, 37, 52, 52, 52, 52, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 44, 45, 46, 43, 24, 25] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42])
total number of confs: 362
number of broken/clashed sets: 130
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057351 none CCOC(=O)NC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 172, 119, 172, 52, 52, 52, 52, 52, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 201, 119, 52, 52, 52, 52, 52, 15, 7, 1, 1, 1, 1, 52, 52, 52, 52] 201
rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46])
total number of confs: 577
number of broken/clashed sets: 130
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057351 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057351
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057351/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057351
Building REAL300000057352
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057352'
/scratch/stefan/7769638/working/building/REAL300000057352 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057352

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057352/0 /scratch/stefan/7769638/working/building/REAL300000057352 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 367)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/367
`/scratch/stefan/7769638/working/3D/367' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC2CC2=CC=CC=N2)C=C1)

`REAL300000057352.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057352.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057352/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057352 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC2CC2=CC=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 13, 13, 13, 30, 30, 30, 30, 30, 30, 58, 75, 75, 75, 75, 75, 1, 1, 1, 1, 8, 13, 30, 30, 30, 30, 30, 30, 30, 58, 58, 75, 75, 75, 75, 1, 1] 75
rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057352 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC2CC2=CC=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [30, 25, 30, 22, 30, 30, 22, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 30, 30, 30, 30, 22, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 30, 30] 76
rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057352 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC2CC2=CC=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 74, 76, 76, 74, 41, 41, 41, 16, 16, 16, 16, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 74, 41, 16, 16, 16, 16, 16, 16, 16, 7, 7, 1, 1, 1, 1, 76, 76] 76
rigid atoms, others: [39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44])
total number of confs: 236
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057352 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057352
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057352/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057352
Building REAL300000057353
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057353'
/scratch/stefan/7769638/working/building/REAL300000057353 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057353

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057353/0 /scratch/stefan/7769638/working/building/REAL300000057353 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 368)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/368
`/scratch/stefan/7769638/working/3D/368' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2CCCC(C(F)(F)F)C2)C=C1)

`REAL300000057353.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057353.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057353/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057353 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCCC(C(F)(F)F)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 36, 36, 86, 86, 86, 86, 86, 86, 86, 86, 86, 1, 1, 1, 1, 8, 14, 36, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 1, 1] 86
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057353 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCCC(C(F)(F)F)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [93, 92, 93, 92, 93, 93, 92, 30, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 93, 93, 93, 93, 92, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93] 93
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 40, 41])
total number of confs: 258
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057353 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057353
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057353/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057353
Building REAL300000057354
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057354'
/scratch/stefan/7769638/working/building/REAL300000057354 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057354

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057354/0 /scratch/stefan/7769638/working/building/REAL300000057354 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 369)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/369
`/scratch/stefan/7769638/working/3D/369' -> `0.mol2'
Preparing input files

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

`REAL300000057354.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057354.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057354/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057354 none COC(=O)CC(C)(C)CC(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 151, 201, 99, 37, 99, 99, 14, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 151, 151, 99, 99, 99, 99, 99, 99, 37, 37, 14, 14, 14, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 855
number of broken/clashed sets: 195
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057354 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057354
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057354/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057354
Building REAL300000057355
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057355'
/scratch/stefan/7769638/working/building/REAL300000057355 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057355

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057355/0 /scratch/stefan/7769638/working/building/REAL300000057355 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 370)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/370
`/scratch/stefan/7769638/working/3D/370' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCC1)

`REAL300000057355.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057355.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057355/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057355 none COC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [75, 69, 33, 33, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 69, 106, 106, 106, 106, 75, 75, 75, 69, 33, 15, 7, 1, 1, 1, 1, 106, 106, 106, 106, 106, 106, 106, 106, 106] 106
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 358
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057355 none COC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [19, 8, 1, 8, 42, 42, 59, 59, 59, 103, 106, 106, 103, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 19, 19, 19, 8, 42, 59, 103, 106, 106, 106, 106, 1, 1, 1, 1, 1, 1, 1, 1, 1] 106
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 331
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057355 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057355
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057355/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057355
Building REAL300000057356
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057356'
/scratch/stefan/7769638/working/building/REAL300000057356 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057356

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057356/0 /scratch/stefan/7769638/working/building/REAL300000057356 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 371)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/371
`/scratch/stefan/7769638/working/3D/371' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C(F)(F)F)N=C3CCCCN32)C=C1)

`REAL300000057356.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057356.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057356/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057356 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C(F)(F)F)N=C3CCCCN32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 32, 32, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 8, 12, 32, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1] 51
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 94
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057356 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C(F)(F)F)N=C3CCCCN32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [57, 56, 57, 56, 57, 57, 56, 25, 25, 25, 10, 10, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 56, 25, 10, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57] 57
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 41, 42])
total number of confs: 162
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057356 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057356
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057356/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057356
Building REAL300000057357
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057357'
/scratch/stefan/7769638/working/building/REAL300000057357 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057357

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057357/0 /scratch/stefan/7769638/working/building/REAL300000057357 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 372)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/372
`/scratch/stefan/7769638/working/3D/372' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C(C)(C)C)

`REAL300000057357.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057357.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057357/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057357 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 11, 27, 53, 53, 53, 53, 53, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 53
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 21, 22, 23, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 147
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057357 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 32, 32, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 32, 18, 7, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53] 53
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 110
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057357 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057357
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057357/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057357
Building REAL300000057358
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057358'
/scratch/stefan/7769638/working/building/REAL300000057358 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057358

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057358/0 /scratch/stefan/7769638/working/building/REAL300000057358 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 373)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/373
`/scratch/stefan/7769638/working/3D/373' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(CC3CCC3)=C2)C=C1)

`REAL300000057358.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057358.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057358/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057358 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(CC3CCC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 11, 11, 11, 21, 21, 72, 72, 21, 72, 72, 134, 201, 201, 201, 72, 1, 1, 1, 1, 8, 11, 21, 72, 72, 34, 134, 134, 201, 201, 201, 201, 201, 201, 201, 72, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 799
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057358 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(CC3CCC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 66, 71, 63, 71, 71, 63, 32, 32, 32, 13, 13, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 1, 71, 71, 71, 71, 63, 32, 13, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 15, 15, 1, 71, 71] 201
rigid atoms, others: [32, 33, 43, 12, 13, 14, 15, 16, 17, 18, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45])
total number of confs: 288
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057358 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(CC3CCC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 201, 200, 101, 101, 101, 59, 59, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 15, 201, 201, 201, 201, 200, 101, 59, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 15, 201, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45])
total number of confs: 605
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057358 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057358
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057358/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057358
Building REAL300000057359
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057359'
/scratch/stefan/7769638/working/building/REAL300000057359 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057359

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057359/0 /scratch/stefan/7769638/working/building/REAL300000057359 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 374)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/374
`/scratch/stefan/7769638/working/3D/374' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=NC=CC=C23)C=C1)

`REAL300000057359.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057359/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057359 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=NC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 8, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 44
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057359 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=NC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 18
rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 22, 23, 24, 25, 26, 27, 37])
total number of confs: 43
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057359 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057359
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057359/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057359
Building REAL300000057360
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057360'
/scratch/stefan/7769638/working/building/REAL300000057360 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057360

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057360/0 /scratch/stefan/7769638/working/building/REAL300000057360 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 375)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/375
`/scratch/stefan/7769638/working/3D/375' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(=O)NC=C2)C=C1)

`REAL300000057360.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057360.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057360/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057360 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(=O)NC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', '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, 11, 8, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 26, 26, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 8, 13, 26, 51, 51, 51, 51, 1, 1] 51
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 104
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057360 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(=O)NC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', '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, 11, 8, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 31, 30, 31, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 30, 12, 1, 1, 1, 1, 52, 52] 52
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 149
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057360 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057360
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057360/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057360
Building REAL300000057361
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057361'
/scratch/stefan/7769638/working/building/REAL300000057361 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057361

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057361/0 /scratch/stefan/7769638/working/building/REAL300000057361 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 376)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/376
`/scratch/stefan/7769638/working/3D/376' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2CCC3=CC=CC=C3C2)C=C1)

`REAL300000057361.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057361.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057361/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057361 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCC3=CC=CC=C3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 3, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 13
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057361 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCC3=CC=CC=C3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 36, 36, 36, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 36, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68] 68
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, 42, 41, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 187
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057361 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057361
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057361/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057361
Building REAL300000057362
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057362'
/scratch/stefan/7769638/working/building/REAL300000057362 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057362

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057362/0 /scratch/stefan/7769638/working/building/REAL300000057362 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 377)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/377
`/scratch/stefan/7769638/working/3D/377' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057362.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057362.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057362/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057362 none CCOC(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [34, 18, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 24, 24, 24, 46, 55, 55, 46, 53, 55, 55, 55, 55, 1, 35, 35, 35, 34, 34, 1, 1, 1, 11, 24, 46, 55, 55, 55, 55] 130
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 25, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 312
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057362 none CCOC(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 127, 123, 55, 123, 55, 55, 55, 55, 24, 24, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 130, 130, 130, 130, 130, 55, 55, 55, 24, 6, 6, 1, 1, 1, 1] 130
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: 299
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057362 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057362
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057362/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057362
Building REAL300000057363
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057363'
/scratch/stefan/7769638/working/building/REAL300000057363 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057363

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057363/0 /scratch/stefan/7769638/working/building/REAL300000057363 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 378)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/378
`/scratch/stefan/7769638/working/3D/378' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CC3)O2)C=C1)

`REAL300000057363.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057363/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057363 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CC3)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 20, 20, 20, 59, 59, 92, 92, 92, 92, 146, 146, 92, 1, 1, 1, 1, 11, 20, 59, 92, 146, 146, 146, 146, 146, 1, 1] 146
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 357
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057363 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CC3)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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: [91, 89, 91, 81, 91, 91, 81, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 13, 13, 1, 91, 91, 91, 91, 81, 31, 7, 1, 13, 13, 13, 13, 13, 91, 91] 143
rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057363 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CC3)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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, 143, 145, 145, 143, 103, 103, 103, 49, 49, 13, 12, 12, 13, 1, 1, 1, 1, 13, 145, 145, 145, 145, 143, 103, 49, 13, 1, 1, 1, 1, 1, 145, 145] 145
rigid atoms, others: [32, 33, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35])
total number of confs: 421
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057363 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057363
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057363/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057363
Building REAL300000057364
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057364'
/scratch/stefan/7769638/working/building/REAL300000057364 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057364

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057364/0 /scratch/stefan/7769638/working/building/REAL300000057364 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 379)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/379
`/scratch/stefan/7769638/working/3D/379' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC(F)=C(Cl)C=C23)C=C1)

`REAL300000057364.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057364.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057364/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057364 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC(F)=C(Cl)C=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
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, 8, 16, 16, 16, 46, 46, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1, 1, 1, 8, 16, 46, 77, 77, 77, 77, 1, 1] 77
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: 140
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057364 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC(F)=C(Cl)C=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [79, 79, 79, 79, 79, 79, 79, 35, 34, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 34, 10, 1, 1, 1, 1, 79, 79] 79
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 205
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057364 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057364
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057364/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057364
Building REAL300000057365
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057365'
/scratch/stefan/7769638/working/building/REAL300000057365 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057365

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057365/0 /scratch/stefan/7769638/working/building/REAL300000057365 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 380)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/380
`/scratch/stefan/7769638/working/3D/380' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCCO1)

`REAL300000057365.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057365.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057365/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057365 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 12, 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, 4, 7, 6, 4, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 37, 37, 37, 37, 37, 24, 24, 24, 13, 7, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37] 37
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057365 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 12, 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, 4, 7, 6, 4, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [10, 1, 10, 10, 23, 23, 23, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1] 37
rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 39, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 103
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057365 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057365
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057365/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057365
Building REAL300000057366
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057366'
/scratch/stefan/7769638/working/building/REAL300000057366 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057366

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057366/0 /scratch/stefan/7769638/working/building/REAL300000057366 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 381)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/381
`/scratch/stefan/7769638/working/3D/381' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Cl)C=C1O)

`REAL300000057366.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057366.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057366/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057366 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Cl)C=C1O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 10, 10, 26, 26, 26, 66, 72, 72, 66, 69, 72, 72, 72, 72, 1, 1, 1, 1, 1, 3, 3, 3, 1, 10, 26, 66, 72, 72, 72, 72, 1, 2] 144
rigid atoms, others: [1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 36, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057366 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Cl)C=C1O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 42, 42, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 71, 72, 72, 72, 72, 72, 72, 72, 72, 42, 18, 7, 1, 1, 1, 1, 72, 144] 144
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
total number of confs: 277
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057366 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057366
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057366/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057366
Building REAL300000057367
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057367'
/scratch/stefan/7769638/working/building/REAL300000057367 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057367

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057367/0 /scratch/stefan/7769638/working/building/REAL300000057367 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 382)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/382
`/scratch/stefan/7769638/working/3D/382' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(Cl)N=CC=C3S2)C=C1)

`REAL300000057367.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057367.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057367/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057367 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(Cl)N=CC=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 32, 32, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 10, 14, 32, 47, 47, 47, 1, 1] 47
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 23, 24, 25, 26] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 90
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057367 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(Cl)N=CC=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 25, 24, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 24, 8, 1, 1, 1, 47, 47] 47
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 33, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 133
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057367 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057367
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057367/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057367
Building REAL300000057368
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057368'
/scratch/stefan/7769638/working/building/REAL300000057368 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057368

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057368/0 /scratch/stefan/7769638/working/building/REAL300000057368 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 383)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/383
`/scratch/stefan/7769638/working/3D/383' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC2=NC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C12)

`REAL300000057368.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057368.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057368/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057368 none CC1=NOC2=NC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 8, 12, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 2, 2, 2, 1, 7, 27, 49, 49, 49, 49, 49, 1] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 36, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057368 none CC1=NOC2=NC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 8, 12, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 26, 14, 7, 1, 1, 1, 1, 49] 49
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])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057368 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057368
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057368/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057368
Building REAL300000057369
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057369'
/scratch/stefan/7769638/working/building/REAL300000057369 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057369

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057369/0 /scratch/stefan/7769638/working/building/REAL300000057369 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 384)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/384
`/scratch/stefan/7769638/working/3D/384' -> `0.mol2'
Preparing input files

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

`REAL300000057369.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057369.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057369/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057369 none CS(=O)(=O)CCC=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 14, 11, 11, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [123, 104, 123, 123, 88, 26, 26, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 104, 104, 88, 88, 26, 16, 7, 1, 1, 1, 1] 123
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 506
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057369 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057369
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057369/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057369
Building REAL300000057370
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057370'
/scratch/stefan/7769638/working/building/REAL300000057370 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057370

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057370/0 /scratch/stefan/7769638/working/building/REAL300000057370 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 385)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/385
`/scratch/stefan/7769638/working/3D/385' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=NC(Cl)=C3S2)C=C1)

`REAL300000057370.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057370.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057370/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057370 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=NC(Cl)=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 14, 1, 1, 7, 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, 3, 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, 8, 10, 10, 10, 30, 30, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 8, 10, 30, 41, 41, 41, 1, 1] 41
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 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])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057370 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=NC(Cl)=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 14, 1, 1, 7, 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, 3, 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, 41, 21, 21, 21, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 21, 11, 1, 1, 1, 41, 41] 41
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 33, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 107
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057370 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057370
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057370/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057370
Building REAL300000057371
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057371'
/scratch/stefan/7769638/working/building/REAL300000057371 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000057371

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057371/0 /scratch/stefan/7769638/working/building/REAL300000057371 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 386)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/386
`/scratch/stefan/7769638/working/3D/386' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C)

`REAL300000057371.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057371/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057371 none C[N@@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 59
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057371 none C[N@@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 6, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 6, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 14
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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
/scratch/stefan/7769638/working/building/REAL300000057371 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057371/1 /scratch/stefan/7769638/working/building/REAL300000057371 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 387)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/387
`/scratch/stefan/7769638/working/3D/387' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C)

`REAL300000057371.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057371/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057371 none C[N@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057371 none C[N@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 6, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 6, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 14
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 33
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057371 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `2'
/scratch/stefan/7769638/working/building/REAL300000057371/2 /scratch/stefan/7769638/working/building/REAL300000057371 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 2 (index: 388)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/388
`/scratch/stefan/7769638/working/3D/388' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C)

`REAL300000057371.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000057371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057371/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057371 none CN1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057371 none CN1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 7, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18] 18
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057371 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057371
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057371/0.*
2: /scratch/stefan/7769638/working/building/REAL300000057371/2.*
1: /scratch/stefan/7769638/working/building/REAL300000057371/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057371
Building REAL300000057372
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057372'
/scratch/stefan/7769638/working/building/REAL300000057372 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057372

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057372/0 /scratch/stefan/7769638/working/building/REAL300000057372 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 389)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/389
`/scratch/stefan/7769638/working/3D/389' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2(C3CCCCO3)CCC2)C=C1)

`REAL300000057372.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057372.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057372/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057372 none O=C([O-])C1=CC=C(NC(=O)NN=CC2(C3CCCCO3)CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 30, 30, 73, 88, 88, 88, 88, 88, 73, 73, 73, 1, 1, 1, 1, 8, 12, 30, 88, 88, 88, 88, 88, 88, 88, 88, 88, 73, 73, 73, 73, 73, 73, 1, 1] 88
rigid atoms, others: [1, 3, 4, 5, 6, 7, 45, 46, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 235
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057372 none O=C([O-])C1=CC=C(NC(=O)NN=CC2(C3CCCCO3)CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 50, 50, 50, 50, 50, 25, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 50, 50] 55
rigid atoms, others: [39, 40, 41, 42, 43, 12, 13, 14, 44, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057372 none O=C([O-])C1=CC=C(NC(=O)NN=CC2(C3CCCCO3)CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 30, 30, 30, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 55, 55, 55, 55, 55, 30, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 55, 55] 55
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 163
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057372 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057372
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057372/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057372
Building REAL300000057373
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057373'
/scratch/stefan/7769638/working/building/REAL300000057373 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057373

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057373/0 /scratch/stefan/7769638/working/building/REAL300000057373 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 390)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/390
`/scratch/stefan/7769638/working/3D/390' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1C(=O)C(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC(C)=CC=C21)

`REAL300000057373.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057373.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057373/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057373 none CCCN1C(=O)C(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC(C)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 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
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 32, 43, 43, 35, 36, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 10, 10, 6, 6, 7, 32, 43, 43, 43, 43, 1, 2, 2, 2, 1, 1] 76
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 41, 45, 46, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44])
total number of confs: 200
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057373 none CCCN1C(=O)C(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC(C)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 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
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 43, 43, 43, 43, 43, 20, 20, 7, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 76, 76, 76, 76, 76, 76, 76, 20, 7, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43] 76
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46])
total number of confs: 283
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057373 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057373
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057373/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057373
Building REAL300000057374
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057374'
/scratch/stefan/7769638/working/building/REAL300000057374 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057374

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057374/0 /scratch/stefan/7769638/working/building/REAL300000057374 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 391)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/391
`/scratch/stefan/7769638/working/3D/391' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(OC(F)(F)F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057374.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057374.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057374/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057374 none COC1=CC=CC(OC(F)(F)F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 1, 1, 13, 13, 30, 30, 30, 66, 87, 87, 66, 77, 87, 87, 87, 87, 4, 4, 4, 1, 1, 1, 13, 29, 66, 87, 87, 87, 87] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 12, 13, 31] set([0, 8, 9, 10, 11, 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: 396
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057374 none COC1=CC=CC(OC(F)(F)F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [125, 87, 87, 87, 87, 87, 87, 87, 184, 201, 201, 201, 22, 22, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 125, 125, 125, 87, 87, 87, 22, 8, 6, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 449
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057374 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057374
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057374/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057374
Building REAL300000057375
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057375'
/scratch/stefan/7769638/working/building/REAL300000057375 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057375

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057375/0 /scratch/stefan/7769638/working/building/REAL300000057375 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 392)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/392
`/scratch/stefan/7769638/working/3D/392' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CCC2=CC=CC(C(F)(F)F)=C2)C=C1)

`REAL300000057375.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057375/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057375 none O=C([O-])C1=CC=C(NC(=O)NN=CCC2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 8, 8, 1, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 10, 12, 12, 12, 32, 32, 104, 176, 201, 144, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 10, 12, 32, 104, 104, 201, 201, 144, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 37] set([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: 686
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057375 none O=C([O-])C1=CC=C(NC(=O)NN=CCC2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 8, 8, 1, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 197, 101, 101, 101, 51, 51, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 201, 201, 201, 201, 197, 101, 51, 8, 8, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 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, 37, 38])
total number of confs: 621
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057375 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057375
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057375/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057375
Building REAL300000057376
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057376'
/scratch/stefan/7769638/working/building/REAL300000057376 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057376

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057376/0 /scratch/stefan/7769638/working/building/REAL300000057376 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 393)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/393
`/scratch/stefan/7769638/working/3D/393' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NC=C1Br)

`REAL300000057376.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057376.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057376/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057376 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NC=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 7, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 2, 2, 2, 1, 7, 9, 25, 25, 25, 25, 25, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 34, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 71
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057376 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NC=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 20, 20, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 20, 8, 5, 1, 1, 1, 1, 25] 25
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 52
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057376 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057376
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057376/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057376
Building REAL300000057377
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057377'
/scratch/stefan/7769638/working/building/REAL300000057377 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057377

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057377/0 /scratch/stefan/7769638/working/building/REAL300000057377 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 394)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/394
`/scratch/stefan/7769638/working/3D/394' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Br)C=C1F)

`REAL300000057377.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057377.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057377/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057377 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Br)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 16, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 16, 36, 36, 36, 36, 36, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 35, 19, 20, 21, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057377 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Br)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 30, 30, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 30, 34, 36, 36, 36, 36, 30, 12, 7, 1, 1, 1, 1, 36] 36
rigid atoms, others: [32, 33, 34, 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, 35])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057377 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057377
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057377/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057377
Building REAL300000057378
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057378'
/scratch/stefan/7769638/working/building/REAL300000057378 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057378

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057378/0 /scratch/stefan/7769638/working/building/REAL300000057378 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 395)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/395
`/scratch/stefan/7769638/working/3D/395' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=NC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057378.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057378.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057378/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057378 none COC1=CC=NC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 33, 33, 33, 55, 59, 59, 55, 56, 59, 59, 59, 59, 1, 2, 2, 2, 1, 1, 10, 10, 10, 32, 55, 59, 59, 59, 59, 1] 61
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 38, 23, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 190
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057378 none COC1=CC=NC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 59, 59, 57, 59, 59, 40, 40, 40, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 59, 61, 61, 61, 59, 59, 40, 40, 40, 16, 7, 1, 1, 1, 1, 59] 61
rigid atoms, others: [34, 35, 36, 37, 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, 38])
total number of confs: 121
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057378 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057378
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057378/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057378
Building REAL300000057379
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057379'
/scratch/stefan/7769638/working/building/REAL300000057379 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057379

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057379/0 /scratch/stefan/7769638/working/building/REAL300000057379 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 396)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/396
`/scratch/stefan/7769638/working/3D/396' -> `0.mol2'
Preparing input files

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

`REAL300000057379.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057379.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057379/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057379 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(C(C)C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [46, 46, 19, 19, 7, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 143, 143, 46, 143, 143, 159, 159, 143, 46, 46, 46, 19, 7, 1, 1, 1, 1, 143, 143, 46, 159, 159, 159, 159, 159, 159, 159, 143] 159
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 451
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057379 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(C(C)C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 1, 12, 12, 53, 54, 54, 142, 143, 143, 143, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 1, 4, 4, 1, 13, 13, 13, 53, 142, 143, 143, 143, 143, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 1] 159
rigid atoms, others: [1, 34, 35, 36, 44, 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, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 395
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057379 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057379
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057379/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057379
Building REAL300000057380
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057380'
/scratch/stefan/7769638/working/building/REAL300000057380 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057380

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057380/0 /scratch/stefan/7769638/working/building/REAL300000057380 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 397)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/397
`/scratch/stefan/7769638/working/3D/397' -> `0.mol2'
Preparing input files

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

`REAL300000057380.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057380.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057380/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057380 none CCCC(C)CCCC(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 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, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 201, 174, 107, 174, 89, 76, 16, 16, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 174, 107, 107, 107, 107, 76, 76, 16, 16, 16, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 14, 22, 23, 47, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 1065
number of broken/clashed sets: 197
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057380 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057380
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057380/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057380
Building REAL300000057381
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057381'
/scratch/stefan/7769638/working/building/REAL300000057381 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057381

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057381/0 /scratch/stefan/7769638/working/building/REAL300000057381 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 398)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/398
`/scratch/stefan/7769638/working/3D/398' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCC1)

`REAL300000057381.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057381/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057381 none COCCCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 6, 6, 1, 1, 1, 13, 13, 27, 27, 27, 56, 70, 70, 56, 56, 70, 70, 70, 70, 1, 1, 1, 33, 33, 33, 14, 14, 6, 6, 6, 6, 13, 27, 56, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [4, 5, 6, 40, 41, 42, 43, 44, 45, 21, 22, 23] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 356
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057381 none COCCCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 120, 120, 70, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 70, 70, 70, 201, 201, 201, 201, 201, 120, 120, 120, 120, 14, 6, 6, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45])
total number of confs: 819
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057381 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057381
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057381/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057381
Building REAL300000057382
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057382'
/scratch/stefan/7769638/working/building/REAL300000057382 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057382

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057382/0 /scratch/stefan/7769638/working/building/REAL300000057382 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 399)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/399
`/scratch/stefan/7769638/working/3D/399' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057382.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057382/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057382 none CC(C)(C)OC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 26, 32, 32, 12, 1, 12, 1, 1, 1, 1, 1, 9, 9, 29, 30, 30, 63, 75, 75, 70, 75, 75, 75, 75, 75, 1, 33, 33, 33, 33, 32, 33, 33, 33, 33, 1, 1, 9, 29, 63, 75, 75, 75, 75] 201
rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 26, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 321
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057382 none CC(C)(C)OC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
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, 129, 75, 129, 75, 75, 75, 28, 28, 8, 8, 7, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 75, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 75, 28, 8, 7, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 408
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057382 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057382
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057382/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057382
Building REAL300000057383
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057383'
/scratch/stefan/7769638/working/building/REAL300000057383 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057383

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057383/0 /scratch/stefan/7769638/working/building/REAL300000057383 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 400)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/400
`/scratch/stefan/7769638/working/3D/400' -> `0.mol2'
Preparing input files

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

`REAL300000057383.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057383/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057383 none CCC(F)(F)C(C)(C)C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 15, 15, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 37, 33, 41, 41, 14, 33, 33, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 33, 33, 33, 33, 33, 33, 14, 6, 6, 1, 1, 1, 1] 41
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 181
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057383 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057383
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057383/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057383
Building REAL300000057384
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057384'
/scratch/stefan/7769638/working/building/REAL300000057384 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057384

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057384/0 /scratch/stefan/7769638/working/building/REAL300000057384 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 401)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/401
`/scratch/stefan/7769638/working/3D/401' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=NN1)

`REAL300000057384.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057384.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057384/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057384 none CCC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 10, 10, 38, 39, 39, 74, 78, 78, 76, 78, 78, 78, 78, 78, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 38, 74, 78, 78, 78, 78, 1] 101
rigid atoms, others: [1, 2, 3, 4, 35, 19, 20, 21, 22] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 235
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057384 none CCC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Cl)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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]
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, 78, 78, 44, 44, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 78, 78, 78, 78, 101, 101, 101, 101, 101, 44, 17, 7, 1, 1, 1, 1, 78] 101
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 275
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057384 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057384
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057384/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057384
Building REAL300000057385
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057385'
/scratch/stefan/7769638/working/building/REAL300000057385 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057385

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057385/0 /scratch/stefan/7769638/working/building/REAL300000057385 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 402)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/402
`/scratch/stefan/7769638/working/3D/402' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(Cl)N1C)

`REAL300000057385.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057385.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057385/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057385 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(Cl)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 16, 8, 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, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 32, 32, 32, 32, 32, 32, 22, 22, 22, 12, 7, 1, 1, 1, 1, 32, 32, 32, 32] 32
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 66
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057385 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(Cl)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 16, 8, 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, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [10, 1, 10, 10, 21, 21, 21, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 32, 32, 32, 32, 32, 1, 2, 2, 2] 32
rigid atoms, others: [32, 1, 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, 33, 34, 35])
total number of confs: 93
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057385 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057385
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057385/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057385
Building REAL300000057386
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057386'
/scratch/stefan/7769638/working/building/REAL300000057386 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000057386

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057386/0 /scratch/stefan/7769638/working/building/REAL300000057386 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 403)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/403
`/scratch/stefan/7769638/working/3D/403' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CN3CC2CCC3)C=C1)

`REAL300000057386.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057386/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057386 none O=C([O-])C1=CC=C(NC(=O)NN=C2CN3CC2CCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 8, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057386 none O=C([O-])C1=CC=C(NC(=O)NN=C2CN3CC2CCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19
rigid atoms, others: [32, 33, 34, 35, 36, 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, 8, 9, 20, 21, 22, 23, 24, 25, 38, 37])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057386 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057386/1 /scratch/stefan/7769638/working/building/REAL300000057386 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 404)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/404
`/scratch/stefan/7769638/working/3D/404' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C[N@@H+]3CC2CCC3)C=C1)

`REAL300000057386.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057386/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057386 none O=C([O-])C1=CC=C(NC(=O)NN=C2C[N@@H+]3CC2CCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 8, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 21, 22, 23, 24, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057386 none O=C([O-])C1=CC=C(NC(=O)NN=C2C[N@@H+]3CC2CCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 23
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, 39, 21, 22, 23, 24, 25, 26, 38])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057386 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `2'
/scratch/stefan/7769638/working/building/REAL300000057386/2 /scratch/stefan/7769638/working/building/REAL300000057386 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 2 (index: 405)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/405
`/scratch/stefan/7769638/working/3D/405' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C[N@H+]3CC2CCC3)C=C1)

`REAL300000057386.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000057386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057386/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057386 none O=C([O-])C1=CC=C(NC(=O)NN=C2C[N@H+]3CC2CCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 8, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 21, 22, 23, 24, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057386 none O=C([O-])C1=CC=C(NC(=O)NN=C2C[N@H+]3CC2CCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 23
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, 39, 21, 22, 23, 24, 25, 26, 38])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057386 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057386
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057386/0.*
2: /scratch/stefan/7769638/working/building/REAL300000057386/2.*
1: /scratch/stefan/7769638/working/building/REAL300000057386/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057386
Building REAL300000057387
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057387'
/scratch/stefan/7769638/working/building/REAL300000057387 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057387

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057387/0 /scratch/stefan/7769638/working/building/REAL300000057387 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 406)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/406
`/scratch/stefan/7769638/working/3D/406' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CN(C(=O)OC(C)(C)C)CC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057387.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057387.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057387/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057387 none CC1CN(C(=O)OC(C)(C)C)CC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 3, 3, 7, 9, 9, 9, 1, 1, 1, 1, 9, 10, 10, 33, 37, 37, 33, 33, 37, 37, 37, 37, 2, 2, 2, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 9, 33, 37, 37, 37, 37] 107
rigid atoms, others: [0, 1, 2, 3, 4, 32, 42, 11, 12, 13, 14, 43, 30, 31] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49])
total number of confs: 164
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057387 none CC1CN(C(=O)OC(C)(C)C)CC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [37, 37, 37, 37, 37, 63, 63, 107, 107, 107, 107, 37, 37, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 37, 107, 107, 107, 107, 107, 107, 107, 107, 107, 37, 37, 12, 7, 1, 1, 1, 1] 107
rigid atoms, others: [49, 46, 47, 48, 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, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 241
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057387 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057387
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057387/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057387
Building REAL300000057388
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057388'
/scratch/stefan/7769638/working/building/REAL300000057388 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057388

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057388/0 /scratch/stefan/7769638/working/building/REAL300000057388 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 407)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/407
`/scratch/stefan/7769638/working/3D/407' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C2N=CS3)C=C1)

`REAL300000057388.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057388.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057388/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057388 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C2N=CS3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 8, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1] 15
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057388 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C2N=CS3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', '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, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 8, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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, 4, 3, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 15, 15] 15
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 21, 22, 23, 24, 25, 26])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057388 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057388
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057388/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057388
Building REAL300000057389
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057389'
/scratch/stefan/7769638/working/building/REAL300000057389 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057389

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057389/0 /scratch/stefan/7769638/working/building/REAL300000057389 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 408)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/408
`/scratch/stefan/7769638/working/3D/408' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC=C1C)

`REAL300000057389.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057389.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057389/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057389 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 5, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [56, 35, 35, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 35, 81, 81, 81, 54, 81, 81, 81, 56, 56, 56, 56, 56, 16, 7, 1, 1, 1, 1, 81, 81, 81, 81, 54, 81, 81, 81, 81] 81
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 334
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057389 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 5, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 10, 1, 10, 10, 38, 38, 38, 80, 81, 81, 80, 80, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 38, 80, 81, 81, 81, 81, 1, 2, 2, 2, 1, 1, 2, 2, 2] 81
rigid atoms, others: [2, 36, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 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, 37, 38, 39, 42, 43, 44])
total number of confs: 296
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057389 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057389
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057389/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057389
Building REAL300000057390
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057390'
/scratch/stefan/7769638/working/building/REAL300000057390 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057390

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057390/0 /scratch/stefan/7769638/working/building/REAL300000057390 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 409)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/409
`/scratch/stefan/7769638/working/3D/409' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(C)C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000057390.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057390.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057390/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057390 none CC1=CC=C(C(C)C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', '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.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']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 35, 35, 61, 61, 61, 107, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 2, 2, 2, 1, 1, 7, 8, 8, 8, 35, 61, 107, 107, 107, 107, 107, 1, 1] 107
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 22, 23, 27, 28] set([6, 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])
total number of confs: 334
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057390 none CC1=CC=C(C(C)C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', '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.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']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 21, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 3, 1, 1, 1, 1, 21, 21] 21
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057390 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057390
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057390/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057390
Building REAL300000057391
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057391'
/scratch/stefan/7769638/working/building/REAL300000057391 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057391

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057391/0 /scratch/stefan/7769638/working/building/REAL300000057391 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 410)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/410
`/scratch/stefan/7769638/working/3D/410' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(O)C=CC=C2Br)C=C1)

`REAL300000057391.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057391/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057391 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(O)C=CC=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 16, 16, 16, 26, 26, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 8, 16, 26, 128, 64, 64, 64, 1, 1] 128
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 243
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057391 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(O)C=CC=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 38, 38, 38, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 38, 12, 2, 1, 1, 1, 66, 66] 132
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 171
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057391 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057391
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057391/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057391
Building REAL300000057392
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057392'
/scratch/stefan/7769638/working/building/REAL300000057392 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057392

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057392/0 /scratch/stefan/7769638/working/building/REAL300000057392 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 411)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/411
`/scratch/stefan/7769638/working/3D/411' -> `0.mol2'
Preparing input files

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

`REAL300000057392.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057392/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057392 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(SC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'S.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: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 75, 75, 75, 75, 75, 201, 201, 201, 201, 75, 16, 16, 16, 6, 6, 1, 1, 1, 1, 75, 75, 75, 75] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 280
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057392 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(SC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'S.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: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 25, 25, 57, 75, 75, 57, 70, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 12, 25, 24, 25, 1, 11, 11, 11, 25, 57, 75, 75, 75, 75, 1, 1, 1, 1] 201
rigid atoms, others: [1, 36, 37, 38, 39, 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])
total number of confs: 365
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057392 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057392
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057392/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057392
Building REAL300000057393
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057393'
/scratch/stefan/7769638/working/building/REAL300000057393 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057393

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057393/0 /scratch/stefan/7769638/working/building/REAL300000057393 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 412)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/412
`/scratch/stefan/7769638/working/3D/412' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057393.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057393.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057393/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057393 none CNC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 1, 1, 1, 1, 4, 12, 26, 26, 26, 26, 26] 26
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057393 none CNC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 26, 20, 26, 26, 20, 20, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 20, 14, 7, 1, 1, 1, 1] 26
rigid atoms, others: [34, 35, 36, 37, 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])
total number of confs: 81
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057393 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057393
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057393/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057393
Building REAL300000057394
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057394'
/scratch/stefan/7769638/working/building/REAL300000057394 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057394

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057394/0 /scratch/stefan/7769638/working/building/REAL300000057394 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 413)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/413
`/scratch/stefan/7769638/working/3D/413' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(C=CNC3=O)O2)C=C1)

`REAL300000057394.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057394.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057394/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057394 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(C=CNC3=O)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 10, 10, 10, 30, 30, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 8, 10, 30, 41, 41, 41, 41, 1, 1] 41
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: 78
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057394 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(C=CNC3=O)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 14, 6, 1, 1, 1, 1, 41, 41] 41
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 114
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057394 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057394
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057394/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057394
Building REAL300000057395
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057395'
/scratch/stefan/7769638/working/building/REAL300000057395 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057395

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057395/0 /scratch/stefan/7769638/working/building/REAL300000057395 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 414)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/414
`/scratch/stefan/7769638/working/3D/414' -> `0.mol2'
Preparing input files

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

`REAL300000057395.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057395/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057395 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(Br)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 16, 1, 1, 7, 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, 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, 8, 12, 12, 12, 26, 26, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 8, 12, 26, 32, 32, 32, 1, 1] 32
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057395 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(Br)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 16, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 18, 18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 18, 8, 1, 1, 1, 36, 36] 36
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 101
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057395 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057395
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057395/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057395
Building REAL300000057396
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057396'
/scratch/stefan/7769638/working/building/REAL300000057396 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057396

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057396/0 /scratch/stefan/7769638/working/building/REAL300000057396 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 415)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/415
`/scratch/stefan/7769638/working/3D/415' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(CNC(=O)OC(C)(C)C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057396.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057396.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057396/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057396 none CCOCC(CNC(=O)OC(C)(C)C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 35, 23, 14, 14, 14, 30, 109, 158, 158, 181, 181, 181, 181, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 23, 23, 30, 30, 109, 181, 181, 181, 181, 181, 181, 181, 181, 181, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [51, 50, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 52] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 605
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057396 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057396
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057396/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057396
Building REAL300000057397
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057397'
/scratch/stefan/7769638/working/building/REAL300000057397 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057397

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057397/0 /scratch/stefan/7769638/working/building/REAL300000057397 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 416)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/416
`/scratch/stefan/7769638/working/3D/416' -> `0.mol2'
Preparing input files

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

`REAL300000057397.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057397/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057397 none CCC(C)C1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 1, 7, 1, 1, 1, 1, 1, 12, 12, 12, 63, 63, 63, 131, 137, 137, 131, 133, 137, 137, 137, 137, 1, 1, 11, 11, 11, 11, 11, 7, 7, 7, 7, 1, 1, 13, 13, 13, 62, 131, 137, 137, 137, 137, 1, 1] 139
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 46, 47, 24, 25, 36] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 453
number of broken/clashed sets: 98
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057397 none CCC(C)C1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [139, 139, 136, 139, 89, 137, 137, 39, 39, 39, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 137, 137, 139, 139, 139, 139, 139, 139, 139, 139, 139, 137, 137, 39, 39, 39, 16, 7, 1, 1, 1, 1, 137, 137] 139
rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47])
total number of confs: 392
number of broken/clashed sets: 98
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057397 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057397
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057397/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057397
Building REAL300000057398
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057398'
/scratch/stefan/7769638/working/building/REAL300000057398 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057398

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057398/0 /scratch/stefan/7769638/working/building/REAL300000057398 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 417)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/417
`/scratch/stefan/7769638/working/3D/417' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1(C)C)

`REAL300000057398.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057398.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057398/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057398 none C[N@@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 2, 2, 2] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 41, 39, 40, 20, 21, 22, 23, 27, 28, 29, 30, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 57
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057398 none C[N@@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 7, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17] 17
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 41
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057398 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057398/1 /scratch/stefan/7769638/working/building/REAL300000057398 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 418)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/418
`/scratch/stefan/7769638/working/3D/418' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1(C)C)

`REAL300000057398.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057398.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057398/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057398 none C[N@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 2, 2, 2] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 41, 39, 40, 20, 21, 22, 23, 27, 28, 29, 30, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 57
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057398 none C[N@H+]1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 7, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17] 17
rigid atoms, others: [33, 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, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 37
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057398 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057398
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057398/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057398/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057398
Building REAL300000057399
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057399'
/scratch/stefan/7769638/working/building/REAL300000057399 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057399

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057399/0 /scratch/stefan/7769638/working/building/REAL300000057399 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 419)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/419
`/scratch/stefan/7769638/working/3D/419' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)SC(C)=C1)

`REAL300000057399.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057399.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057399/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057399 none CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)SC(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 14, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [115, 106, 51, 51, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 51, 140, 140, 140, 140, 140, 140, 117, 117, 117, 117, 117, 106, 106, 16, 7, 1, 1, 1, 1, 140, 140, 140, 140, 140, 140, 140] 163
rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 549
number of broken/clashed sets: 84
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057399 none CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)SC(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 14, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [39, 30, 9, 1, 9, 9, 45, 45, 45, 119, 140, 140, 119, 131, 140, 140, 140, 140, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 30, 30, 44, 119, 140, 140, 140, 140, 2, 2, 2, 2, 2, 2, 1] 163
rigid atoms, others: [3, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 627
number of broken/clashed sets: 84
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057399 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057399
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057399/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057399
Building REAL300000057400
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057400'
/scratch/stefan/7769638/working/building/REAL300000057400 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057400

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057400/0 /scratch/stefan/7769638/working/building/REAL300000057400 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 420)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/420
`/scratch/stefan/7769638/working/3D/420' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C2=NC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CS2)C=N1)

`REAL300000057400.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057400.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057400/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057400 none CN1C=C(C2=NC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CS2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 5, 20, 20, 41, 41, 41, 85, 88, 88, 85, 88, 88, 88, 88, 88, 4, 5, 1, 1, 2, 2, 2, 1, 20, 41, 85, 88, 88, 88, 88, 4, 1] 88
rigid atoms, others: [0, 1, 2, 3, 4, 38, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 260
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057400 none CN1C=C(C2=NC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CS2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [5, 4, 4, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 60, 65, 65, 60, 64, 65, 65, 65, 65, 1, 1, 4, 4, 5, 5, 5, 5, 9, 27, 60, 65, 65, 65, 65, 1, 5] 88
rigid atoms, others: [3, 4, 5, 6, 7, 22, 23, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057400 none CN1C=C(C2=NC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CS2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 65, 65, 65, 39, 39, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 65, 65, 88, 88, 88, 88, 88, 88, 39, 12, 7, 1, 1, 1, 1, 65, 88] 88
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 154
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057400 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057400
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057400/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057400
Building REAL300000057401
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057401'
/scratch/stefan/7769638/working/building/REAL300000057401 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057401

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057401/0 /scratch/stefan/7769638/working/building/REAL300000057401 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 421)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/421
`/scratch/stefan/7769638/working/3D/421' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC(C)=CS1)

`REAL300000057401.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057401.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057401/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057401 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC(C)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 5, 1, 14, 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, 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
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 31, 31, 31, 31, 31, 24, 24, 24, 10, 7, 1, 1, 1, 1, 31, 31, 31, 31] 31
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 34, 33, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 58
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057401 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC(C)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 5, 1, 14, 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, 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
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [13, 1, 13, 13, 17, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 13, 13, 13, 17, 31, 31, 31, 31, 31, 2, 2, 2, 1] 31
rigid atoms, others: [1, 34, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 87
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057401 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057401
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057401/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057401
Building REAL300000057402
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057402'
/scratch/stefan/7769638/working/building/REAL300000057402 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057402

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057402/0 /scratch/stefan/7769638/working/building/REAL300000057402 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 422)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/422
`/scratch/stefan/7769638/working/3D/422' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1Cl)

`REAL300000057402.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057402.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057402/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057402 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1Cl 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.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, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 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, 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
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 69, 76, 76, 69, 69, 76, 76, 76, 76, 1, 1, 1, 1, 4, 4, 4, 1, 9, 31, 69, 76, 76, 76, 76, 1, 1] 76
rigid atoms, others: [1, 2, 3, 4, 5, 35, 20, 21, 22, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 253
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057402 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1Cl 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.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, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 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, 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
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, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 76, 76, 76, 76, 76, 76, 76, 76, 34, 16, 7, 1, 1, 1, 1, 76, 76] 76
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 138
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057402 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057402
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057402/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057402
Building REAL300000057403
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057403'
/scratch/stefan/7769638/working/building/REAL300000057403 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057403

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057403/0 /scratch/stefan/7769638/working/building/REAL300000057403 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 423)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/423
`/scratch/stefan/7769638/working/3D/423' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC2=C1OCCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057403.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057403/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057403 none COC1=CC=CC2=C1OCCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 16, 20, 20, 18, 20, 20, 20, 20, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 20, 20, 20, 20] 20
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057403 none COC1=CC=CC2=C1OCCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 7, 1, 1, 1, 1] 20
rigid atoms, others: [41, 42, 43, 44, 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, 38, 39, 40])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057403 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057403
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057403/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057403
Building REAL300000057404
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057404'
/scratch/stefan/7769638/working/building/REAL300000057404 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057404

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057404/0 /scratch/stefan/7769638/working/building/REAL300000057404 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 424)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/424
`/scratch/stefan/7769638/working/3D/424' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CC2CCC2)C=C1)

`REAL300000057404.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057404/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057404 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CC2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 81, 81, 81, 81, 81, 159, 201, 201, 201, 1, 1, 1, 1, 8, 8, 24, 81, 81, 159, 159, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 659
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057404 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CC2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 77, 82, 71, 82, 82, 71, 34, 33, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 82, 82, 82, 82, 71, 33, 9, 1, 1, 5, 5, 19, 19, 19, 19, 19, 19, 19, 82, 82] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 338
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057404 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2CC2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 199, 201, 201, 199, 115, 115, 115, 53, 53, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 115, 53, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42])
total number of confs: 619
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057404 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057404
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057404/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057404
Building REAL300000057405
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057405'
/scratch/stefan/7769638/working/building/REAL300000057405 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057405

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057405/0 /scratch/stefan/7769638/working/building/REAL300000057405 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 425)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/425
`/scratch/stefan/7769638/working/3D/425' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057405.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057405.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057405/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057405 none COC(=O)CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 10, 48, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 31, 31, 27, 27, 31, 31, 31, 31, 1, 1, 48, 48, 48, 10, 10, 1, 1, 1, 1, 1, 8, 21, 31, 31, 31, 31, 1, 1, 1, 1] 148
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 43, 44, 41, 23, 24, 42, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40])
total number of confs: 225
number of broken/clashed sets: 89
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057405 none COC(=O)CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [148, 148, 83, 148, 31, 31, 31, 31, 31, 9, 9, 7, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 148, 148, 148, 83, 83, 31, 31, 31, 31, 31, 9, 7, 1, 1, 1, 1, 31, 31, 31, 31] 148
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44])
total number of confs: 470
number of broken/clashed sets: 89
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057405 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057405
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057405/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057405
Building REAL300000057406
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057406'
/scratch/stefan/7769638/working/building/REAL300000057406 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057406

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057406/0 /scratch/stefan/7769638/working/building/REAL300000057406 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 426)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/426
`/scratch/stefan/7769638/working/3D/426' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1)

`REAL300000057406.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057406.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057406/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057406 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 7, 7, 6, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 1, 1] 5
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 25, 26, 27, 28, 37] 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])
total number of confs: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057406 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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, 40, 41, 41, 40, 19, 19, 19, 8, 8, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 1, 41, 41, 41, 41, 40, 18, 8, 1, 4, 4, 4, 4, 41, 41] 41
rigid atoms, others: [32, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057406 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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, 40, 41, 41, 40, 21, 21, 21, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 41, 41, 41, 41, 40, 21, 13, 4, 1, 1, 1, 1, 41, 41] 41
rigid atoms, others: [33, 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, 37, 38])
total number of confs: 110
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057406 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057406
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057406/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057406
Building REAL300000057407
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057407'
/scratch/stefan/7769638/working/building/REAL300000057407 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057407

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057407/0 /scratch/stefan/7769638/working/building/REAL300000057407 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 427)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/427
`/scratch/stefan/7769638/working/3D/427' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2CC(F)(F)F)C=C1)

`REAL300000057407.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057407.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057407/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057407 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2CC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 17, 17, 17, 39, 39, 118, 118, 39, 118, 118, 118, 160, 160, 160, 160, 1, 1, 1, 1, 10, 17, 39, 118, 118, 39, 118, 160, 160, 1, 1] 160
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 37] set([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: 530
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057407 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2CC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [89, 88, 89, 85, 89, 89, 85, 41, 41, 41, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 89, 89, 89, 89, 85, 41, 12, 1, 1, 1, 1, 6, 6, 89, 89] 112
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 271
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057407 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057407
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057407/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057407
Building REAL300000057408
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057408'
/scratch/stefan/7769638/working/building/REAL300000057408 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057408

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057408/0 /scratch/stefan/7769638/working/building/REAL300000057408 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 428)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/428
`/scratch/stefan/7769638/working/3D/428' -> `0.mol2'
Preparing input files

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

`REAL300000057408.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057408.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057408/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057408 none CCOC(=O)C1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 24, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 10, 10, 36, 50, 50, 42, 42, 50, 50, 50, 50, 1, 51, 51, 51, 51, 51, 2, 2, 2, 1, 1, 9, 36, 50, 50, 50, 50, 1, 1] 201
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 40, 41, 23] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 334
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057408 none CCOC(=O)C1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 193, 180, 50, 180, 50, 50, 50, 50, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 201, 50, 50, 50, 50, 50, 18, 7, 1, 1, 1, 1, 50, 50] 201
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 501
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057408 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057408
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057408/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057408
Building REAL300000057409
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057409'
/scratch/stefan/7769638/working/building/REAL300000057409 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057409

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057409/0 /scratch/stefan/7769638/working/building/REAL300000057409 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 429)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/429
`/scratch/stefan/7769638/working/3D/429' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Br)=N1)

`REAL300000057409.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057409.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057409/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057409 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Br)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 20, 21, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 2, 2, 2, 1, 8, 20, 41, 41, 41, 41, 41] 41
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 119
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057409 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(Br)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 28, 28, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 28, 10, 7, 1, 1, 1, 1] 41
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 78
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057409 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057409
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057409/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057409
Building REAL300000057410
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057410'
/scratch/stefan/7769638/working/building/REAL300000057410 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057410

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057410/0 /scratch/stefan/7769638/working/building/REAL300000057410 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 430)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/430
`/scratch/stefan/7769638/working/3D/430' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1)

`REAL300000057410.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057410.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057410/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057410 none O=C([O-])C1=CC=C(NC(=O)NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 4, 6, 6, 6, 11, 11, 33, 44, 44, 44, 44, 44, 44, 11, 25, 25, 25, 25, 25, 1, 1, 1, 1, 4, 6, 33, 33, 44, 44, 44, 44, 44, 44, 44, 25, 25, 25, 25, 1, 1] 48
rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 47, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057410 none O=C([O-])C1=CC=C(NC(=O)NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [146, 146, 146, 142, 146, 146, 127, 63, 63, 63, 29, 29, 7, 3, 1, 1, 1, 1, 1, 1, 1, 29, 65, 65, 65, 65, 65, 146, 146, 146, 146, 127, 63, 7, 7, 3, 3, 1, 1, 1, 1, 1, 65, 65, 65, 65, 146, 146] 201
rigid atoms, others: [37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47])
total number of confs: 506
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057410 none O=C([O-])C1=CC=C(NC(=O)NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 57, 61, 61, 54, 23, 23, 23, 8, 8, 1, 8, 47, 60, 65, 65, 63, 65, 65, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 54, 23, 47, 47, 60, 60, 65, 65, 65, 65, 65, 1, 1, 1, 1, 61, 61] 201
rigid atoms, others: [44, 42, 43, 12, 45, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47])
total number of confs: 428
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057410 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057410
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057410/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057410
Building REAL300000057411
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057411'
/scratch/stefan/7769638/working/building/REAL300000057411 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057411

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057411/0 /scratch/stefan/7769638/working/building/REAL300000057411 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 431)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/431
`/scratch/stefan/7769638/working/3D/431' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C=C1)

`REAL300000057411.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057411.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057411/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057411 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 2, 2, 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, 11, 17, 17, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 11, 17, 24, 24, 24, 24, 24, 24, 24, 1, 1] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 37] set([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: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057411 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 2, 2, 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, 24, 10, 9, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 24, 24, 24, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 24, 24] 24
rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 21, 22, 24, 25, 26, 27, 28, 29, 37])
total number of confs: 69
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057411 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057411
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057411/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057411
Building REAL300000057412
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057412'
/scratch/stefan/7769638/working/building/REAL300000057412 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057412

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057412/0 /scratch/stefan/7769638/working/building/REAL300000057412 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 432)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/432
`/scratch/stefan/7769638/working/3D/432' -> `0.mol2'
Preparing input files

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

`REAL300000057412.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057412.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057412/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057412 none CN(C)C1=CC=C(C#N)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 1, 6, 6, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 1, 1, 1, 6, 10, 28, 28, 28, 28, 28] 28
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 9, 10, 7, 11] set([0, 2, 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])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057412 none CN(C)C1=CC=C(C#N)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 22, 22, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 22, 12, 7, 1, 1, 1, 1] 28
rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 59
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057412 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057412
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057412/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057412
Building REAL300000057413
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057413'
/scratch/stefan/7769638/working/building/REAL300000057413 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057413

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057413/0 /scratch/stefan/7769638/working/building/REAL300000057413 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 433)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/433
`/scratch/stefan/7769638/working/3D/433' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)(F)F)C=C2[N+](=O)[O-])C=C1)

`REAL300000057413.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057413.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057413/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057413 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)(F)F)C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 1, 1, 7, 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, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 32, 32, 42, 42, 41, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 8, 14, 32, 42, 42, 42, 1, 1] 42
rigid atoms, others: [1, 3, 4, 5, 6, 7, 36, 26, 27, 28, 29, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35])
total number of confs: 90
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057413 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)(F)F)C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 1, 1, 7, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 45, 45, 45, 45, 45, 20, 7, 1, 1, 1, 45, 45] 45
rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057413 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057413
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057413/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057413
Building REAL300000057414
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057414'
/scratch/stefan/7769638/working/building/REAL300000057414 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057414

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057414/0 /scratch/stefan/7769638/working/building/REAL300000057414 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 434)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/434
`/scratch/stefan/7769638/working/3D/434' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1)

`REAL300000057414.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057414.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057414/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057414 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 6, 6, 10, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 2, 2, 2, 1, 1, 6, 10, 29, 29, 29, 29, 29, 1] 29
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: 89
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057414 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [29, 28, 29, 29, 24, 24, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 24, 10, 7, 1, 1, 1, 1, 29] 29
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057414 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057414
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057414/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057414
Building REAL300000057415
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057415'
/scratch/stefan/7769638/working/building/REAL300000057415 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057415

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057415/0 /scratch/stefan/7769638/working/building/REAL300000057415 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 435)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/435
`/scratch/stefan/7769638/working/3D/435' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057415.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057415.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057415/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057415 none CC(=O)NC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 57, 60, 60, 60, 60, 60, 60, 60, 60, 1, 5, 5, 5, 5, 1, 1, 1, 11, 25, 57, 60, 60, 60, 60, 1] 107
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39, 24, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057415 none CC(=O)NC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 60, 60, 60, 60, 60, 36, 36, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 107, 107, 107, 107, 60, 60, 60, 36, 16, 7, 1, 1, 1, 1, 60] 107
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, 39])
total number of confs: 268
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057415 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057415
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057415/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057415
Building REAL300000057416
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057416'
/scratch/stefan/7769638/working/building/REAL300000057416 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057416

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057416/0 /scratch/stefan/7769638/working/building/REAL300000057416 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 436)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/436
`/scratch/stefan/7769638/working/3D/436' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Cl)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC)

`REAL300000057416.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057416/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057416 none COC1=CC(Cl)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 28, 28, 73, 87, 87, 79, 87, 87, 87, 87, 87, 1, 1, 1, 3, 4, 4, 4, 1, 10, 28, 73, 87, 87, 87, 87, 1, 4, 4, 4] 106
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 29, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 287
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057416 none COC1=CC(Cl)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 87, 87, 87, 87, 87, 46, 46, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 87, 87, 87, 106, 106, 106, 106, 87, 46, 17, 7, 1, 1, 1, 1, 87, 106, 106, 106] 106
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 224
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057416 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057416
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057416/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057416
Building REAL300000057417
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057417'
/scratch/stefan/7769638/working/building/REAL300000057417 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057417

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057417/0 /scratch/stefan/7769638/working/building/REAL300000057417 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 437)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/437
`/scratch/stefan/7769638/working/3D/437' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC2=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CN=C21)

`REAL300000057417.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057417.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057417/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057417 none CN1N=CC2=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CN=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 2, 2, 2, 1, 1, 7, 19, 45, 45, 45, 45, 45, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 28, 29, 37] set([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: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057417 none CN1N=CC2=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CN=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 24, 24, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 24, 8, 5, 1, 1, 1, 1, 45] 45
rigid atoms, others: [33, 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, 37])
total number of confs: 86
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057417 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057417
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057417/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057417
Building REAL300000057418
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057418'
/scratch/stefan/7769638/working/building/REAL300000057418 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057418

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057418/0 /scratch/stefan/7769638/working/building/REAL300000057418 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 438)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/438
`/scratch/stefan/7769638/working/3D/438' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(Br)C=C2F)C=C1)

`REAL300000057418.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057418.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057418/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057418 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(Br)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 34, 34, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 8, 14, 34, 50, 50, 1, 1] 50
rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057418 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(Br)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 21, 20, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 20, 6, 1, 1, 58, 58] 58
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 155
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057418 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057418
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057418/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057418
Building REAL300000057419
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057419'
/scratch/stefan/7769638/working/building/REAL300000057419 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057419

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057419/0 /scratch/stefan/7769638/working/building/REAL300000057419 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 439)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/439
`/scratch/stefan/7769638/working/3D/439' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCOC3)N=N2)C=C1)

`REAL300000057419.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057419.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057419/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057419 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCOC3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 13, 13, 30, 30, 44, 44, 44, 140, 201, 201, 201, 201, 44, 44, 1, 1, 1, 1, 8, 13, 30, 44, 140, 140, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 695
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057419 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCOC3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 44, 38, 44, 44, 38, 18, 18, 18, 5, 5, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 1, 1, 44, 44, 44, 44, 38, 17, 5, 1, 8, 8, 23, 23, 23, 23, 23, 23, 23, 44, 44] 201
rigid atoms, others: [12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057419 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCOC3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 197, 201, 201, 197, 109, 109, 109, 63, 63, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 23, 23, 201, 201, 201, 201, 197, 109, 63, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42])
total number of confs: 624
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057419 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057419
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057419/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057419
Building REAL300000057420
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057420'
/scratch/stefan/7769638/working/building/REAL300000057420 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057420

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057420/0 /scratch/stefan/7769638/working/building/REAL300000057420 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 440)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/440
`/scratch/stefan/7769638/working/3D/440' -> `0.mol2'
Preparing input files

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

`REAL300000057420.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057420.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057420/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057420 none CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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, 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: [66, 57, 28, 28, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 58, 58, 58, 58, 58, 58, 66, 66, 66, 66, 66, 57, 57, 10, 7, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58] 77
rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43])
total number of confs: 300
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057420 none CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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, 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: [24, 20, 8, 1, 8, 8, 26, 26, 26, 47, 58, 58, 47, 52, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 20, 20, 26, 47, 58, 58, 58, 58, 1, 2, 2, 2, 1, 1] 77
rigid atoms, others: [3, 38, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41])
total number of confs: 308
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057420 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057420
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057420/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057420
Building REAL300000057421
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057421'
/scratch/stefan/7769638/working/building/REAL300000057421 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057421

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057421/0 /scratch/stefan/7769638/working/building/REAL300000057421 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 441)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/441
`/scratch/stefan/7769638/working/3D/441' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(CC(F)(F)F)C=C2)C=C1)

`REAL300000057421.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057421.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057421/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057421 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(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', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8, 26, 26, 28, 28, 28, 28, 49, 49, 49, 49, 28, 28, 1, 1, 1, 1, 7, 8, 26, 28, 28, 49, 49, 28, 28, 1, 1] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 37] set([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: 160
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057421 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(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', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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: [28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 28, 28, 28, 28, 28, 14, 4, 1, 1, 4, 4, 1, 1, 28, 28] 49
rigid atoms, others: [32, 35, 36, 12, 13, 14, 15, 16, 17, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057421 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057421
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057421/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057421
Building REAL300000057422
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057422'
/scratch/stefan/7769638/working/building/REAL300000057422 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057422

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057422/0 /scratch/stefan/7769638/working/building/REAL300000057422 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 442)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/442
`/scratch/stefan/7769638/working/3D/442' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C2CCCCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057422.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057422.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057422/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057422 none CN1N=C2CCCCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 43, 45, 45, 43, 45, 45, 45, 45, 45, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 43, 45, 45, 45, 45] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 32, 33, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 132
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057422 none CN1N=C2CCCCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 45, 45, 30, 30, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 30, 14, 7, 1, 1, 1, 1] 45
rigid atoms, others: [39, 40, 41, 42, 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, 36, 37, 38])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057422 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057422
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057422/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057422
Building REAL300000057423
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057423'
/scratch/stefan/7769638/working/building/REAL300000057423 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057423

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057423/0 /scratch/stefan/7769638/working/building/REAL300000057423 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 443)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/443
`/scratch/stefan/7769638/working/3D/443' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CS1)

`REAL300000057423.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057423.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057423/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057423 none CC1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 9, 9, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 2, 2, 2, 2, 2, 2, 9, 29, 48, 48, 48, 48, 48, 1] 48
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 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])
total number of confs: 147
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057423 none CC1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 34, 34, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 34, 14, 7, 1, 1, 1, 1, 48] 48
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057423 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057423
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057423/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057423
Building REAL300000057424
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057424'
/scratch/stefan/7769638/working/building/REAL300000057424 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057424

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057424/0 /scratch/stefan/7769638/working/building/REAL300000057424 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 444)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/444
`/scratch/stefan/7769638/working/3D/444' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(F)=C2)C=C1)

`REAL300000057424.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057424.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057424/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057424 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 1, 15, 1, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 8, 8, 8, 24, 24, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 6, 8, 24, 45, 45, 45, 1, 1] 45
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057424 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 1, 15, 1, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 19, 18, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 18, 6, 1, 1, 1, 46, 46] 46
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, 31])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057424 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057424
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057424/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057424
Building REAL300000057425
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057425'
/scratch/stefan/7769638/working/building/REAL300000057425 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057425

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057425/0 /scratch/stefan/7769638/working/building/REAL300000057425 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 445)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/445
`/scratch/stefan/7769638/working/3D/445' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1)

`REAL300000057425.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057425.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057425/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057425 none CCOC(=O)C1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 12, 1, 12, 1, 1, 1, 1, 1, 12, 12, 37, 38, 38, 70, 84, 84, 77, 84, 84, 84, 84, 84, 1, 1, 1, 35, 35, 35, 35, 35, 2, 2, 2, 12, 37, 70, 84, 84, 84, 84, 2, 2, 2, 1] 201
rigid atoms, others: [3, 5, 6, 7, 8, 9, 45, 24, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 386
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057425 none CCOC(=O)C1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 187, 183, 84, 183, 84, 84, 84, 22, 22, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 84, 84, 84, 201, 201, 201, 201, 201, 84, 84, 84, 22, 8, 6, 1, 1, 1, 1, 84, 84, 84, 84] 201
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 502
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057425 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057425
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057425/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057425
Building REAL300000057426
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057426'
/scratch/stefan/7769638/working/building/REAL300000057426 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057426

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057426/0 /scratch/stefan/7769638/working/building/REAL300000057426 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 446)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/446
`/scratch/stefan/7769638/working/3D/446' -> `0.mol2'
Preparing input files

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

`REAL300000057426.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057426.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057426/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057426 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC=C(Cl)C=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Cl', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 28, 29, 29, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 28, 70, 70, 70, 70, 70, 1, 1, 1] 70
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 19, 20, 21, 22, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 30, 31, 32, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057426 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC=C(Cl)C=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Cl', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 43, 43, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 43, 16, 7, 1, 1, 1, 1, 70, 70, 70] 70
rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057426 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057426
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057426/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057426
Building REAL300000057427
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057427'
/scratch/stefan/7769638/working/building/REAL300000057427 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057427

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057427/0 /scratch/stefan/7769638/working/building/REAL300000057427 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 447)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/447
`/scratch/stefan/7769638/working/3D/447' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1)

`REAL300000057427.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057427.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057427/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057427 none CCOC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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: [25, 13, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 46, 62, 62, 53, 62, 62, 62, 62, 62, 1, 25, 25, 25, 25, 25, 1, 1, 6, 16, 46, 62, 62, 62, 62, 1] 111
rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 24, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057427 none CCOC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 103, 103, 62, 103, 62, 62, 62, 44, 44, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 62, 111, 111, 111, 111, 111, 62, 62, 44, 18, 7, 1, 1, 1, 1, 62] 111
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 299
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057427 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057427
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057427/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057427
Building REAL300000057428
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057428'
/scratch/stefan/7769638/working/building/REAL300000057428 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057428

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057428/0 /scratch/stefan/7769638/working/building/REAL300000057428 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 448)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/448
`/scratch/stefan/7769638/working/3D/448' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CNC2=CC=CC=C12)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057428.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057428.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057428/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057428 none CC(CCC1=CNC2=CC=CC=C12)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 119, 119, 119, 197, 201, 201, 197, 201, 201, 201, 201, 201, 45, 45, 45, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 119, 197, 201, 201, 201, 201] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 36, 38, 39, 37] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45])
total number of confs: 649
number of broken/clashed sets: 159
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057428 none CC(CCC1=CNC2=CC=CC=C12)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 105, 119, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 105, 105, 119, 119, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [42, 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])
total number of confs: 561
number of broken/clashed sets: 159
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057428 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057428
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057428/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057428
Building REAL300000057429
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057429'
/scratch/stefan/7769638/working/building/REAL300000057429 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057429

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057429/0 /scratch/stefan/7769638/working/building/REAL300000057429 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 449)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/449
`/scratch/stefan/7769638/working/3D/449' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NC(N)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057429.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057429.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057429/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057429 none CC1=CC=NC(N)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 4, 7, 6, 4, 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
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, 12, 12, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 2, 2, 1, 1, 2, 2, 12, 30, 46, 46, 46, 46, 46] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 139
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057429 none CC1=CC=NC(N)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 4, 7, 6, 4, 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
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, 22, 22, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 22, 14, 7, 1, 1, 1, 1] 46
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: 84
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057429 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057429/1 /scratch/stefan/7769638/working/building/REAL300000057429 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 450)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/450
`/scratch/stefan/7769638/working/3D/450' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=[NH+]C(N)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057429.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057429.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057429/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057429 none CC1=CC=[NH+]C(N)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 6, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 4, 7, 6, 4, 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
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, 8, 8, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 1, 2, 2, 8, 14, 24, 24, 24, 24, 24] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28] set([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: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057429 none CC1=CC=[NH+]C(N)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 6, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 4, 7, 6, 4, 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
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, 24, 24, 18, 18, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 24, 24, 24, 24, 24, 24, 18, 10, 7, 1, 1, 1, 1] 24
rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057429 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057429
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057429/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057429/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057429
Building REAL300000057430
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057430'
/scratch/stefan/7769638/working/building/REAL300000057430 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057430

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057430/0 /scratch/stefan/7769638/working/building/REAL300000057430 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 451)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/451
`/scratch/stefan/7769638/working/3D/451' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCNC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057430.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057430.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057430/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057430 none CCNC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 28, 30, 30, 28, 29, 30, 30, 30, 30, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 4, 12, 28, 30, 30, 30, 30] 32
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057430 none CCNC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 30, 30, 30, 22, 30, 30, 18, 18, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 30, 30, 30, 30, 18, 12, 7, 1, 1, 1, 1] 32
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 110
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057430 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057430
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057430/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057430
Building REAL300000057431
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057431'
/scratch/stefan/7769638/working/building/REAL300000057431 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057431

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057431/0 /scratch/stefan/7769638/working/building/REAL300000057431 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 452)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/452
`/scratch/stefan/7769638/working/3D/452' -> `0.mol2'
Preparing input files

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

`REAL300000057431.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057431.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057431/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057431 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 1, 8, 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, 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
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 22, 22, 22, 22, 22, 20, 20, 20, 10, 7, 1, 1, 1, 1, 22, 22, 22, 22, 22] 22
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35])
total number of confs: 50
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057431 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 1, 8, 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, 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
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 7, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 22, 22, 22, 22, 22, 1, 2, 2, 2, 1] 22
rigid atoms, others: [1, 35, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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
/scratch/stefan/7769638/working/building/REAL300000057431 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057431
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057431/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057431
Building REAL300000057432
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057432'
/scratch/stefan/7769638/working/building/REAL300000057432 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057432

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057432/0 /scratch/stefan/7769638/working/building/REAL300000057432 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 453)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/453
`/scratch/stefan/7769638/working/3D/453' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CN=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C)

`REAL300000057432.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057432.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057432/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057432 none COC1=CN=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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]
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: [4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 34, 34, 34, 81, 90, 90, 88, 88, 90, 90, 90, 90, 1, 1, 4, 4, 4, 1, 1, 10, 34, 81, 90, 90, 90, 90, 2, 2, 2] 90
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22, 23, 27, 28] set([0, 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])
total number of confs: 261
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057432 none COC1=CN=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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]
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, 40, 40, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 90, 90, 90, 90, 90, 90, 90, 40, 18, 7, 1, 1, 1, 1, 90, 90, 90] 90
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 156
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057432 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057432
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057432/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057432
Building REAL300000057433
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057433'
/scratch/stefan/7769638/working/building/REAL300000057433 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057433

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057433/0 /scratch/stefan/7769638/working/building/REAL300000057433 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 454)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/454
`/scratch/stefan/7769638/working/3D/454' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=NC=NC=C23)C=C1)

`REAL300000057433.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057433.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057433/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057433 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=NC=NC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 16, 16, 16, 36, 36, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 8, 16, 36, 55, 55, 55, 55, 1, 1] 55
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: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057433 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=NC=NC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 27, 26, 27, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 26, 10, 1, 1, 1, 1, 54, 54] 54
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, 34, 33, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 145
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057433 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057433
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057433/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057433
Building REAL300000057434
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057434'
/scratch/stefan/7769638/working/building/REAL300000057434 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057434

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057434/0 /scratch/stefan/7769638/working/building/REAL300000057434 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 455)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/455
`/scratch/stefan/7769638/working/3D/455' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C)=C1)

`REAL300000057434.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057434.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057434/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057434 none CC1=CC(CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 4, 10, 10, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 2, 2, 2, 1, 4, 4, 10, 12, 25, 25, 25, 25, 25, 1, 2, 2, 2, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 37, 41, 20, 21, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 91
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057434 none CC1=CC(CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 21, 7, 7, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 21, 25, 25, 25, 25, 21, 21, 7, 5, 3, 1, 1, 1, 1, 25, 25, 25, 25, 21] 25
rigid atoms, others: [33, 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, 37, 38, 39, 40, 41])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057434 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057434
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057434/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057434
Building REAL300000057435
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057435'
/scratch/stefan/7769638/working/building/REAL300000057435 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057435

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057435/0 /scratch/stefan/7769638/working/building/REAL300000057435 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 456)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/456
`/scratch/stefan/7769638/working/3D/456' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057435.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057435.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057435/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057435 none CC(C)(C)OC(=O)NC1CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 15, 8, 15, 1, 1, 1, 1, 1, 13, 13, 16, 16, 16, 38, 48, 48, 38, 45, 48, 48, 48, 48, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 1, 1, 1, 1, 13, 16, 38, 48, 48, 48, 48, 1, 1] 201
rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 48, 40, 49, 26] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 240
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057435 none CC(C)(C)OC(=O)NC1CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 184, 140, 184, 48, 48, 48, 8, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 48, 48, 48, 48, 8, 6, 6, 1, 1, 1, 1, 48, 48] 201
rigid atoms, others: [44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49])
total number of confs: 571
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057435 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057435
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057435/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057435
Building REAL300000057436
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057436'
/scratch/stefan/7769638/working/building/REAL300000057436 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057436

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057436/0 /scratch/stefan/7769638/working/building/REAL300000057436 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 457)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/457
`/scratch/stefan/7769638/working/3D/457' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(N2CCC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2)C=N1)

`REAL300000057436.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057436.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057436/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057436 none CN1C=C(N2CCC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 9, 59, 59, 104, 104, 104, 198, 201, 201, 198, 198, 201, 201, 201, 201, 9, 1, 1, 2, 2, 2, 1, 9, 9, 9, 9, 9, 59, 104, 198, 201, 201, 201, 201, 9, 9, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 44, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 575
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057436 none CN1C=C(N2CCC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 1, 1, 13, 13, 38, 38, 38, 89, 99, 99, 89, 89, 99, 99, 99, 99, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 13, 38, 89, 99, 99, 99, 99, 1, 1, 9] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 42, 43, 23, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 44])
total number of confs: 330
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057436 none CN1C=C(N2CCC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 99, 99, 99, 99, 37, 37, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 201, 201, 201, 99, 99, 99, 99, 99, 37, 16, 7, 1, 1, 1, 1, 99, 99, 201] 201
rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44])
total number of confs: 390
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057436 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057436
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057436/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057436
Building REAL300000057437
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057437'
/scratch/stefan/7769638/working/building/REAL300000057437 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057437

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057437/0 /scratch/stefan/7769638/working/building/REAL300000057437 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 458)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/458
`/scratch/stefan/7769638/working/3D/458' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=C(Cl)N=CC=C2O1)

`REAL300000057437.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057437.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057437/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057437 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=C(Cl)N=CC=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.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, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 21, 10, 7, 1, 1, 1, 1, 33, 33, 33] 33
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37])
total number of confs: 64
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057437 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=C(Cl)N=CC=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.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, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 18, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 18, 33, 33, 33, 33, 33, 1, 1, 1] 33
rigid atoms, others: [1, 35, 36, 37, 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])
total number of confs: 99
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057437 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057437
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057437/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057437
Building REAL300000057438
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057438'
/scratch/stefan/7769638/working/building/REAL300000057438 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057438

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057438/0 /scratch/stefan/7769638/working/building/REAL300000057438 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 459)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/459
`/scratch/stefan/7769638/working/3D/459' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(OC)=C1OC)

`REAL300000057438.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057438.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057438/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057438 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(OC)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [84, 44, 44, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 44, 122, 122, 122, 122, 122, 150, 122, 122, 150, 84, 84, 84, 84, 84, 16, 7, 1, 1, 1, 1, 122, 122, 122, 150, 150, 150, 150, 150, 150] 166
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 496
number of broken/clashed sets: 97
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057438 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(OC)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 11, 1, 11, 11, 41, 41, 41, 107, 122, 122, 114, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 1, 3, 1, 1, 4, 27, 27, 27, 27, 27, 41, 107, 122, 122, 122, 122, 1, 1, 1, 3, 3, 3, 5, 5, 5] 166
rigid atoms, others: [2, 38, 39, 40, 17, 18, 19, 20, 21, 22, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46])
total number of confs: 436
number of broken/clashed sets: 97
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057438 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057438
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057438/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057438
Building REAL300000057439
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057439'
/scratch/stefan/7769638/working/building/REAL300000057439 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057439

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057439/0 /scratch/stefan/7769638/working/building/REAL300000057439 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 460)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/460
`/scratch/stefan/7769638/working/3D/460' -> `0.mol2'
Preparing input files

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

`REAL300000057439.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057439/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057439 none CC(C)(C)OC(=O)N[C@H]1C[C@@H](C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 25, 15, 8, 15, 1, 1, 1, 1, 1, 1, 1, 13, 13, 15, 15, 15, 37, 47, 47, 37, 37, 47, 47, 47, 47, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 1, 1, 13, 15, 37, 47, 47, 47, 47, 1, 1] 201
rigid atoms, others: [49, 7, 8, 9, 10, 11, 12, 13, 48, 40, 39, 28] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057439 none CC(C)(C)OC(=O)N[C@H]1C[C@@H](C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 182, 138, 182, 47, 47, 47, 47, 8, 47, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 47, 47, 8, 6, 6, 1, 1, 1, 1, 47, 47] 201
rigid atoms, others: [44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49])
total number of confs: 569
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057439 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057439
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057439/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057439
Building REAL300000057440
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057440'
/scratch/stefan/7769638/working/building/REAL300000057440 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057440

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057440/0 /scratch/stefan/7769638/working/building/REAL300000057440 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 461)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/461
`/scratch/stefan/7769638/working/3D/461' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCCO1)

`REAL300000057440.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057440.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057440/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057440 none CC(C)(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 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, 7, 4, 7, 6, 4, 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
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [55, 18, 55, 18, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 55, 72, 72, 72, 72, 72, 55, 55, 55, 55, 55, 55, 18, 6, 6, 1, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 72] 72
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057440 none CC(C)(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 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, 7, 4, 7, 6, 4, 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
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 8, 32, 32, 47, 47, 47, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 32, 47, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1] 72
rigid atoms, others: [1, 37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 219
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057440 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057440
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057440/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057440
Building REAL300000057441
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057441'
/scratch/stefan/7769638/working/building/REAL300000057441 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057441

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057441/0 /scratch/stefan/7769638/working/building/REAL300000057441 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 462)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/462
`/scratch/stefan/7769638/working/3D/462' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)C1(C)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057441.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057441.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057441/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057441 none C[NH+](C)C1(C)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 24, 31, 31, 28, 28, 31, 31, 31, 31, 1, 1, 6, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 1, 9, 24, 31, 31, 31, 31, 1, 1, 1, 1] 33
rigid atoms, others: [1, 34, 35, 4, 5, 6, 7, 8, 9, 10, 44, 45, 46, 47, 23, 24, 36, 37] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43])
total number of confs: 122
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057441 none C[NH+](C)C1(C)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 31, 33, 33, 31, 31, 31, 31, 31, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 33, 33, 33, 33, 33, 33, 31, 31, 31, 31, 31, 31, 31, 10, 7, 1, 1, 1, 1, 31, 31, 31, 31] 33
rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47])
total number of confs: 66
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057441 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057441
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057441/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057441
Building REAL300000057442
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057442'
/scratch/stefan/7769638/working/building/REAL300000057442 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057442

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057442/0 /scratch/stefan/7769638/working/building/REAL300000057442 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 463)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/463
`/scratch/stefan/7769638/working/3D/463' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C(C2CCC2)C2CCCO2)C=C1)

`REAL300000057442.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057442.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057442/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057442 none O=C([O-])C1=CC=C(NC(=O)NN=C(C2CCC2)C2CCCO2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 40, 40, 64, 64, 64, 40, 73, 73, 73, 73, 1, 1, 1, 1, 9, 19, 64, 64, 64, 64, 64, 64, 64, 73, 73, 73, 73, 73, 73, 73, 1, 1] 75
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 43, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 265
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057442 none O=C([O-])C1=CC=C(NC(=O)NN=C(C2CCC2)C2CCCO2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 32, 33, 33, 30, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 33, 33, 33, 33, 30, 16, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 33, 33] 44
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 140
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057442 none O=C([O-])C1=CC=C(NC(=O)NN=C(C2CCC2)C2CCCO2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 42, 23, 23, 23, 10, 10, 1, 10, 19, 19, 19, 1, 1, 1, 1, 1, 43, 43, 43, 43, 42, 23, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 43, 43] 44
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 12, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43])
total number of confs: 161
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057442 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057442
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057442/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057442
Building REAL300000057443
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057443'
/scratch/stefan/7769638/working/building/REAL300000057443 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057443

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057443/0 /scratch/stefan/7769638/working/building/REAL300000057443 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 464)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/464
`/scratch/stefan/7769638/working/3D/464' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(Cl)C(F)=C2)C=C1)

`REAL300000057443.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057443.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057443/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057443 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(Cl)C(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 16, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 10, 10, 10, 26, 26, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 6, 10, 26, 51, 51, 1, 1] 51
rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 104
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057443 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(Cl)C(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 16, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 19, 18, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 18, 6, 1, 1, 51, 51] 51
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 137
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057443 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057443
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057443/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057443
Building REAL300000057444
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057444'
/scratch/stefan/7769638/working/building/REAL300000057444 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057444

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057444/0 /scratch/stefan/7769638/working/building/REAL300000057444 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 465)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/465
`/scratch/stefan/7769638/working/3D/465' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)C=C1)

`REAL300000057444.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057444.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057444/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057444 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 9
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057444 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 32, 31, 32, 10, 10, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 59, 59, 59, 59, 59, 31, 10, 1, 1, 4, 4, 1, 4, 4, 1, 59, 59] 59
rigid atoms, others: [33, 34, 40, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057444 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 33, 33, 33, 17, 17, 3, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 59, 59, 59, 59, 59, 33, 17, 4, 4, 1, 1, 1, 1, 1, 4, 59, 59] 59
rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 175
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057444 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057444
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057444/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057444
Building REAL300000057445
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057445'
/scratch/stefan/7769638/working/building/REAL300000057445 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057445

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057445/0 /scratch/stefan/7769638/working/building/REAL300000057445 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 466)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/466
`/scratch/stefan/7769638/working/3D/466' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Br)C(F)=C2F)C=C1)

`REAL300000057445.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057445.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057445/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057445 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Br)C(F)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 17, 1, 15, 1, 15, 1, 1, 7, 7, 6, 6, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 9, 9, 9, 22, 22, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 7, 9, 22, 27, 27, 1, 1] 27
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057445 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Br)C(F)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 17, 1, 15, 1, 15, 1, 1, 7, 7, 6, 6, 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, 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, 16, 16, 16, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 16, 10, 1, 1, 31, 31] 31
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 83
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057445 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057445
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057445/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057445
Building REAL300000057446
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057446'
/scratch/stefan/7769638/working/building/REAL300000057446 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057446

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057446/0 /scratch/stefan/7769638/working/building/REAL300000057446 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 467)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/467
`/scratch/stefan/7769638/working/3D/467' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NC=C(Br)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057446.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057446.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057446/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057446 none COC1=NC=C(Br)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 8, 1, 1, 17, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 3, 3, 3, 1, 1, 8, 14, 28, 28, 28, 28, 28] 28
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057446 none COC1=NC=C(Br)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 8, 1, 1, 17, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 24, 24, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 28, 28, 28, 28, 24, 14, 7, 1, 1, 1, 1] 28
rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 62
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057446 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057446
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057446/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057446
Building REAL300000057447
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057447'
/scratch/stefan/7769638/working/building/REAL300000057447 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057447

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057447/0 /scratch/stefan/7769638/working/building/REAL300000057447 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 468)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/468
`/scratch/stefan/7769638/working/3D/468' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)OC(C)(C)C)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057447.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057447.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057447/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057447 none CN1N=C(C(=O)OC(C)(C)C)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 24, 31, 32, 31, 1, 1, 1, 10, 10, 32, 32, 32, 61, 73, 73, 69, 73, 73, 73, 73, 73, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 10, 31, 61, 73, 73, 73, 73] 201
rigid atoms, others: [0, 1, 2, 3, 4, 40, 11, 12, 13] set([5, 6, 7, 8, 9, 10, 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, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 316
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057447 none CN1N=C(C(=O)OC(C)(C)C)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 73, 73, 142, 142, 201, 201, 201, 201, 73, 28, 28, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 73, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 28, 8, 6, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 422
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057447 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057447
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057447/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057447
Building REAL300000057448
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057448'
/scratch/stefan/7769638/working/building/REAL300000057448 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057448

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057448/0 /scratch/stefan/7769638/working/building/REAL300000057448 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 469)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/469
`/scratch/stefan/7769638/working/3D/469' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(Br)SC=C2)C=C1)

`REAL300000057448.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057448.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057448/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057448 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(Br)SC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', '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, 11, 8, 8, 1, 1, 1, 17, 14, 1, 1, 1, 1, 7, 7, 6, 6, 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, 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, 10, 10, 10, 10, 30, 30, 34, 34, 34, 34, 34, 1, 1, 1, 1, 10, 10, 30, 34, 34, 1, 1] 34
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 54
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057448 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(Br)SC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', '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, 11, 8, 8, 1, 1, 1, 17, 14, 1, 1, 1, 1, 7, 7, 6, 6, 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, 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, 12, 12, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 12, 8, 1, 1, 34, 34] 34
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 28, 29])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057448 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057448
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057448/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057448
Building REAL300000057449
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057449'
/scratch/stefan/7769638/working/building/REAL300000057449 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057449

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057449/0 /scratch/stefan/7769638/working/building/REAL300000057449 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 470)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/470
`/scratch/stefan/7769638/working/3D/470' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1OC)

`REAL300000057449.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057449.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057449/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057449 none CCOC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 9, 1, 1, 1, 1, 1, 10, 10, 26, 27, 27, 70, 84, 84, 70, 77, 84, 84, 84, 84, 1, 1, 1, 1, 1, 3, 34, 34, 34, 34, 34, 1, 10, 26, 70, 84, 84, 84, 84, 1, 4, 4, 4] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 40, 21, 22, 23, 24, 25] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43])
total number of confs: 417
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057449 none CCOC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 177, 84, 84, 84, 38, 38, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 84, 84, 84, 84, 84, 151, 201, 201, 201, 201, 201, 84, 38, 16, 7, 1, 1, 1, 1, 84, 151, 151, 151] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43])
total number of confs: 550
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057449 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057449
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057449/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057449
Building REAL300000057450
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057450'
/scratch/stefan/7769638/working/building/REAL300000057450 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057450

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057450/0 /scratch/stefan/7769638/working/building/REAL300000057450 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 471)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/471
`/scratch/stefan/7769638/working/3D/471' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C3=CC=CC=C23)C=C1)

`REAL300000057450.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057450.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057450/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057450 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C3=CC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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, 1, 1, 1, 1, 11, 17, 17, 17, 40, 40, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 11, 17, 40, 56, 56, 56, 56, 56, 56, 1, 1] 56
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 37] set([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: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057450 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C3=CC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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, 30, 30, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 30, 10, 1, 1, 1, 1, 1, 1, 56, 56] 56
rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 24, 25, 26, 27, 28, 29, 30, 37])
total number of confs: 157
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057450 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057450
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057450/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057450
Building REAL300000057451
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057451'
/scratch/stefan/7769638/working/building/REAL300000057451 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057451

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057451/0 /scratch/stefan/7769638/working/building/REAL300000057451 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 472)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/472
`/scratch/stefan/7769638/working/3D/472' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN=C2Br)C=C1)

`REAL300000057451.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057451.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057451/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057451 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', '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, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 17, 1, 1, 7, 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, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 30, 30, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 8, 13, 30, 36, 36, 36, 1, 1] 36
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 77
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057451 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', '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, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 17, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 16, 8, 1, 1, 1, 38, 38] 38
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, 31])
total number of confs: 113
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057451 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057451
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057451/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057451
Building REAL300000057452
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057452'
/scratch/stefan/7769638/working/building/REAL300000057452 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057452

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057452/0 /scratch/stefan/7769638/working/building/REAL300000057452 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 473)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/473
`/scratch/stefan/7769638/working/3D/473' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)F)N=C2)C=C1)

`REAL300000057452.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057452.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057452/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057452 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)F)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 8, 1, 1, 1, 7, 7, 6, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 34, 34, 56, 56, 56, 56, 76, 76, 56, 56, 1, 1, 1, 1, 8, 14, 34, 56, 56, 76, 56, 1, 1] 76
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: 230
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057452 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)F)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 8, 1, 1, 1, 7, 7, 6, 6, 7, 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, 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: [56, 54, 56, 54, 56, 56, 53, 22, 22, 22, 9, 9, 1, 1, 1, 1, 1, 1, 10, 10, 1, 1, 56, 56, 56, 56, 53, 22, 9, 1, 1, 10, 1, 56, 56] 76
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 33, 34])
total number of confs: 191
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057452 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057452
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057452/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057452
Building REAL300000057453
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057453'
/scratch/stefan/7769638/working/building/REAL300000057453 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057453

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057453/0 /scratch/stefan/7769638/working/building/REAL300000057453 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 474)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/474
`/scratch/stefan/7769638/working/3D/474' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3C=CNC3=C2)C=C1)

`REAL300000057453.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057453.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057453/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057453 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3C=CNC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 24, 24, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 9, 10, 24, 43, 43, 43, 43, 43, 43, 1, 1] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 36] set([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: 78
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057453 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3C=CNC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 20, 19, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 19, 6, 1, 1, 1, 1, 1, 1, 42, 42] 42
rigid atoms, others: [32, 33, 34, 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, 35, 22, 23, 24, 25, 26, 27, 28, 36])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057453 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057453
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057453/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057453
Building REAL300000057454
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057454'
/scratch/stefan/7769638/working/building/REAL300000057454 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057454

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057454/0 /scratch/stefan/7769638/working/building/REAL300000057454 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 475)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/475
`/scratch/stefan/7769638/working/3D/475' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CN=C1F)

`REAL300000057454.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057454.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057454/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057454 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CN=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 10, 10, 23, 23, 23, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 2, 2, 2, 10, 23, 55, 55, 55, 55, 55, 1, 1] 55
rigid atoms, others: [0, 1, 2, 3, 33, 34, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 155
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057454 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CN=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 28, 28, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 28, 14, 7, 1, 1, 1, 1, 55, 55] 55
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 106
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057454 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057454
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057454/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057454
Building REAL300000057455
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057455'
/scratch/stefan/7769638/working/building/REAL300000057455 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057455

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057455/0 /scratch/stefan/7769638/working/building/REAL300000057455 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 476)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/476
`/scratch/stefan/7769638/working/3D/476' -> `0.mol2'
Preparing input files

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

`REAL300000057455.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057455.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057455/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057455 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(F)=C2OC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 18, 18, 18, 40, 40, 124, 124, 124, 124, 124, 124, 124, 187, 187, 187, 187, 1, 1, 1, 1, 9, 18, 40, 124, 124, 124, 1, 1] 187
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 25, 26, 27, 28, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34])
total number of confs: 298
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057455 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(F)=C2OC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 1, 1, 7, 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, 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: [84, 84, 84, 71, 84, 84, 65, 22, 22, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 84, 84, 84, 84, 65, 22, 8, 1, 1, 1, 84, 84] 135
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36])
total number of confs: 328
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057455 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057455
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057455/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057455
Building REAL300000057456
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057456'
/scratch/stefan/7769638/working/building/REAL300000057456 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057456

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057456/0 /scratch/stefan/7769638/working/building/REAL300000057456 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 477)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/477
`/scratch/stefan/7769638/working/3D/477' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OC1=CC=C(F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057456.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057456.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057456/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057456 none CC(C)OC1=CC=C(F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 9, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 56, 68, 68, 63, 68, 68, 68, 68, 68, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 8, 22, 56, 68, 68, 68, 68] 111
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 230
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057456 none CC(C)OC1=CC=C(F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 68, 68, 68, 36, 68, 68, 68, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 68, 36, 68, 34, 16, 7, 1, 1, 1, 1] 111
rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 264
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057456 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057456
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057456/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057456
Building REAL300000057457
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057457'
/scratch/stefan/7769638/working/building/REAL300000057457 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057457

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057457/0 /scratch/stefan/7769638/working/building/REAL300000057457 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 478)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/478
`/scratch/stefan/7769638/working/3D/478' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(F)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057457.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057457/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057457 none CCOC1=CC(F)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 40, 41, 41, 90, 102, 102, 95, 95, 102, 102, 102, 102, 1, 18, 18, 18, 18, 18, 1, 1, 10, 40, 90, 102, 102, 102, 102, 1] 146
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 39, 24, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 382
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057457 none CCOC1=CC(F)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [146, 144, 102, 102, 102, 102, 102, 102, 33, 33, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102, 146, 146, 146, 146, 146, 102, 102, 33, 14, 7, 1, 1, 1, 1, 102] 146
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, 39])
total number of confs: 249
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057457 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057457
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057457/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057457
Building REAL300000057458
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057458'
/scratch/stefan/7769638/working/building/REAL300000057458 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057458

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057458/0 /scratch/stefan/7769638/working/building/REAL300000057458 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 479)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/479
`/scratch/stefan/7769638/working/3D/479' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)C=C1)

`REAL300000057458.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057458.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057458/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057458 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 39, 39, 54, 54, 39, 39, 86, 86, 86, 86, 86, 86, 54, 54, 1, 1, 1, 1, 10, 16, 39, 54, 54, 86, 86, 86, 86, 86, 86, 86, 86, 54, 54, 1, 1] 86
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 46, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 263
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057458 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [54, 46, 54, 46, 54, 54, 46, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 10, 10, 18, 18, 18, 18, 1, 1, 54, 54, 54, 54, 46, 21, 6, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 54, 54] 86
rigid atoms, others: [33, 34, 44, 43, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057458 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [86, 86, 86, 86, 86, 86, 86, 61, 61, 61, 32, 32, 18, 9, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 18, 18, 86, 86, 86, 86, 86, 61, 32, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 86, 86] 86
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 17, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46])
total number of confs: 275
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057458 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057458
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057458/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057458
Building REAL300000057459
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057459'
/scratch/stefan/7769638/working/building/REAL300000057459 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057459

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057459/0 /scratch/stefan/7769638/working/building/REAL300000057459 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 480)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/480
`/scratch/stefan/7769638/working/3D/480' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC(F)F)C=C2F)C=C1)

`REAL300000057459.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057459.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057459/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057459 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC(F)F)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 15, 1, 1, 7, 7, 6, 6, 7, 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, 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, 10, 16, 16, 16, 38, 38, 73, 73, 41, 73, 199, 201, 201, 73, 73, 73, 1, 1, 1, 1, 10, 16, 38, 73, 73, 201, 73, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 24, 25, 26, 27, 36] set([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: 441
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057459 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC(F)F)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 15, 1, 1, 7, 7, 6, 6, 7, 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, 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: [72, 60, 72, 60, 72, 72, 60, 25, 24, 25, 10, 10, 1, 1, 1, 1, 1, 1, 12, 46, 46, 1, 1, 1, 72, 72, 72, 72, 60, 24, 10, 1, 1, 46, 1, 72, 72] 201
rigid atoms, others: [32, 34, 12, 13, 14, 15, 16, 17, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 35, 36])
total number of confs: 391
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057459 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057459
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057459/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057459
Building REAL300000057460
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057460'
/scratch/stefan/7769638/working/building/REAL300000057460 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057460

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057460/0 /scratch/stefan/7769638/working/building/REAL300000057460 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 481)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/481
`/scratch/stefan/7769638/working/3D/481' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057460.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057460.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057460/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057460 none CC(C)(C)OC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 7, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 36, 37, 37, 82, 95, 95, 82, 82, 95, 95, 95, 95, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 11, 36, 82, 95, 95, 95, 95, 1] 146
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 45, 25, 37, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 358
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057460 none CC(C)(C)OC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [146, 146, 146, 146, 95, 95, 95, 95, 95, 37, 37, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 95, 146, 146, 146, 146, 146, 146, 146, 146, 146, 95, 95, 95, 37, 15, 7, 1, 1, 1, 1, 95] 146
rigid atoms, others: [41, 42, 43, 44, 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, 36, 37, 38, 39, 40, 45])
total number of confs: 254
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057460 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057460
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057460/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057460
Building REAL300000057461
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057461'
/scratch/stefan/7769638/working/building/REAL300000057461 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057461

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057461/0 /scratch/stefan/7769638/working/building/REAL300000057461 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 482)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/482
`/scratch/stefan/7769638/working/3D/482' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Cl)C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057461.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057461.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057461/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057461 none CC1=C(Cl)C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2, 1, 1, 1, 9, 19, 38, 38, 38, 38, 38] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28] set([9, 10, 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: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057461 none CC1=C(Cl)C=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 27, 27, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 38, 38, 27, 15, 7, 1, 1, 1, 1] 38
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: 78
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057461 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057461
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057461/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057461
Building REAL300000057462
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057462'
/scratch/stefan/7769638/working/building/REAL300000057462 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057462

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057462/0 /scratch/stefan/7769638/working/building/REAL300000057462 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 483)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/483
`/scratch/stefan/7769638/working/3D/483' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1C)

`REAL300000057462.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057462.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057462/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057462 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 5, 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, 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
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, 11, 11, 25, 25, 25, 44, 47, 47, 45, 45, 47, 47, 47, 47, 1, 1, 1, 1, 1, 4, 4, 4, 1, 11, 25, 44, 47, 47, 47, 47, 1, 2, 2, 2] 47
rigid atoms, others: [1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 36, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057462 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 5, 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, 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
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, 26, 26, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 26, 12, 7, 1, 1, 1, 1, 47, 47, 47, 47] 47
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 88
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057462 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057462
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057462/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057462
Building REAL300000057463
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057463'
/scratch/stefan/7769638/working/building/REAL300000057463 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057463

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057463/0 /scratch/stefan/7769638/working/building/REAL300000057463 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 484)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/484
`/scratch/stefan/7769638/working/3D/484' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1Br)

`REAL300000057463.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057463.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057463/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057463 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1Br 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 9, 9, 21, 21, 21, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 21, 39, 39, 39, 39, 39, 2, 2, 2] 39
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057463 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1Br 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 28, 28, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 28, 16, 7, 1, 1, 1, 1, 39, 39, 39] 39
rigid atoms, others: [32, 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, 36, 37, 38])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057463 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057463
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057463/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057463
Building REAL300000057464
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057464'
/scratch/stefan/7769638/working/building/REAL300000057464 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057464

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057464/0 /scratch/stefan/7769638/working/building/REAL300000057464 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 485)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/485
`/scratch/stefan/7769638/working/3D/485' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Br)

`REAL300000057464.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057464.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057464/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057464 none CC1=CC=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 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
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, 12, 12, 30, 30, 30, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 2, 2, 2, 1, 1, 12, 30, 76, 76, 76, 76, 76] 76
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057464 none CC1=CC=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 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
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, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 76, 76, 76, 76, 76, 76, 76, 34, 16, 7, 1, 1, 1, 1] 76
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 132
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057464 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057464
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057464/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057464
Building REAL300000057465
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057465'
/scratch/stefan/7769638/working/building/REAL300000057465 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057465

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057465/0 /scratch/stefan/7769638/working/building/REAL300000057465 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 486)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/486
`/scratch/stefan/7769638/working/3D/486' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057465.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057465.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057465/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057465 none CC(=O)NCC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [39, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 48, 48, 42, 42, 48, 48, 48, 48, 1, 1, 39, 39, 39, 39, 10, 10, 1, 1, 1, 1, 1, 9, 37, 48, 48, 48, 48, 1, 1, 1, 1] 188
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 43, 44, 45, 23, 24, 42, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 257
number of broken/clashed sets: 110
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057465 none CC(=O)NCC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [188, 188, 188, 150, 48, 48, 48, 48, 48, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 188, 188, 188, 188, 150, 150, 48, 48, 48, 48, 48, 17, 7, 1, 1, 1, 1, 48, 48, 48, 48] 188
rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 635
number of broken/clashed sets: 110
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057465 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057465
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057465/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057465
Building REAL300000057466
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057466'
/scratch/stefan/7769638/working/building/REAL300000057466 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057466

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057466/0 /scratch/stefan/7769638/working/building/REAL300000057466 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 487)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/487
`/scratch/stefan/7769638/working/3D/487' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CC=C(F)C=C1[N+](=O)[O-])=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057466.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057466.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057466/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057466 none CC(CC1=CC=C(F)C=C1[N+](=O)[O-])=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 4, 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
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 1, 1, 1, 3, 5, 5, 5, 5, 5] 5
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34] set([0, 1, 11, 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])
total number of confs: 22
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057466 none CC(CC1=CC=C(F)C=C1[N+](=O)[O-])=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 6, 4, 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
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 2, 1, 1, 1, 1] 5
rigid atoms, others: [37, 38, 39, 40, 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])
total number of confs: 17
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057466 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057466
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057466/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057466
Building REAL300000057467
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057467'
/scratch/stefan/7769638/working/building/REAL300000057467 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057467

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057467/0 /scratch/stefan/7769638/working/building/REAL300000057467 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 488)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/488
`/scratch/stefan/7769638/working/3D/488' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN=CN2CC2=CC=CC=C2)C=C1)

`REAL300000057467.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057467.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057467/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057467 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN=CN2CC2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 33, 33, 59, 59, 59, 59, 59, 145, 161, 161, 145, 161, 161, 1, 1, 1, 1, 8, 13, 33, 59, 145, 145, 161, 161, 145, 161, 161, 1, 1] 161
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 551
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057467 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN=CN2CC2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 60, 60, 59, 60, 60, 54, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 8, 16, 16, 60, 60, 60, 60, 54, 20, 6, 1, 8, 8, 16, 16, 8, 16, 16, 60, 60] 162
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057467 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN=CN2CC2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 162, 162, 162, 153, 72, 72, 72, 26, 26, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 153, 72, 26, 16, 5, 5, 1, 1, 1, 1, 1, 162, 162] 162
rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41])
total number of confs: 459
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057467 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057467
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057467/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057467
Building REAL300000057468
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057468'
/scratch/stefan/7769638/working/building/REAL300000057468 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057468

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057468/0 /scratch/stefan/7769638/working/building/REAL300000057468 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 489)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/489
`/scratch/stefan/7769638/working/3D/489' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCCC1)

`REAL300000057468.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057468.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057468/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057468 none C=CCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [22, 8, 1, 1, 1, 13, 13, 47, 47, 47, 98, 113, 113, 98, 104, 108, 113, 113, 113, 1, 1, 1, 1, 22, 22, 22, 8, 8, 13, 47, 98, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 1, 1] 159
rigid atoms, others: [35, 2, 3, 4, 37, 38, 39, 40, 41, 42, 19, 20, 21, 22, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 465
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057468 none C=CCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [159, 159, 113, 32, 32, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 113, 113, 113, 113, 159, 159, 159, 159, 159, 32, 13, 7, 1, 1, 1, 1, 113, 113, 113, 113, 113, 113, 113, 113] 159
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 514
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057468 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057468
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057468/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057468
Building REAL300000057469
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057469'
/scratch/stefan/7769638/working/building/REAL300000057469 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057469

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057469/0 /scratch/stefan/7769638/working/building/REAL300000057469 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 490)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/490
`/scratch/stefan/7769638/working/3D/490' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NSC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057469.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057469.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057469/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057469 none COC1=NSC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 8, 14, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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, 4, 4, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 4, 12, 24, 24, 24, 24, 24] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057469 none COC1=NSC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 8, 14, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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, 24, 24, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 12, 7, 1, 1, 1, 1] 24
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, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 46
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057469 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057469
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057469/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057469
Building REAL300000057470
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057470'
/scratch/stefan/7769638/working/building/REAL300000057470 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057470

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057470/0 /scratch/stefan/7769638/working/building/REAL300000057470 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 491)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/491
`/scratch/stefan/7769638/working/3D/491' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=CC2=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=CN=C12)

`REAL300000057470.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057470/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057470 none COC(=O)C1=CC=CC2=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=CN=C12 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 12, 39, 39, 39, 94, 107, 107, 94, 94, 107, 107, 107, 107, 1, 1, 1, 1, 11, 11, 11, 1, 1, 1, 12, 39, 94, 107, 107, 107, 107, 1, 1] 151
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 43, 34, 25, 26, 27, 28, 42] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 405
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057470 none COC(=O)C1=CC=CC2=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=CN=C12 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 107, 151, 107, 107, 107, 107, 107, 33, 33, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 151, 151, 151, 107, 107, 107, 33, 12, 7, 1, 1, 1, 1, 107, 107] 151
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43])
total number of confs: 312
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057470 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057470
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057470/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057470
Building REAL300000057471
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057471'
/scratch/stefan/7769638/working/building/REAL300000057471 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057471

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057471/0 /scratch/stefan/7769638/working/building/REAL300000057471 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 492)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/492
`/scratch/stefan/7769638/working/3D/492' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)OC(C)(C)C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057471.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057471.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057471/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057471 none CN1N=CC(C(=O)OC(C)(C)C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 14, 15, 15, 15, 1, 1, 4, 4, 18, 18, 18, 28, 29, 29, 28, 28, 29, 29, 29, 29, 2, 2, 2, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 18, 28, 29, 29, 29, 29] 53
rigid atoms, others: [0, 1, 2, 3, 4, 5, 12, 13, 31] set([6, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 124
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057471 none CN1N=CC(C(=O)OC(C)(C)C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 29, 29, 29, 47, 47, 53, 53, 53, 53, 16, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 29, 29, 29, 53, 53, 53, 53, 53, 53, 53, 53, 53, 16, 6, 6, 1, 1, 1, 1] 53
rigid atoms, others: [44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057471 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057471
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057471/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057471
Building REAL300000057472
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057472'
/scratch/stefan/7769638/working/building/REAL300000057472 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057472

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057472/0 /scratch/stefan/7769638/working/building/REAL300000057472 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 493)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/493
`/scratch/stefan/7769638/working/3D/493' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CC=CC(C)=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057472.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057472.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057472/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057472 none CC(CC1=CC=CC(C)=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 38, 38, 38, 77, 77, 77, 77, 77, 77, 77, 77, 77, 21, 21, 21, 7, 7, 1, 1, 1, 2, 2, 2, 1, 38, 77, 77, 77, 77, 77] 77
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 35, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 228
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057472 none CC(CC1=CC=CC(C)=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 37, 74, 77, 69, 77, 77, 77, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 12, 12, 37, 37, 77, 77, 69, 77, 77, 77, 77, 5, 3, 1, 1, 1, 1] 77
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 237
number of broken/clashed sets: 71
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057472 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057472
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057472/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057472
Building REAL300000057473
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057473'
/scratch/stefan/7769638/working/building/REAL300000057473 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057473

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057473/0 /scratch/stefan/7769638/working/building/REAL300000057473 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 494)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/494
`/scratch/stefan/7769638/working/3D/494' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=C2C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CNC2=CC=C1)

`REAL300000057473.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057473.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057473/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057473 none N#CC1=C2C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CNC2=CC=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 56, 58, 58, 56, 56, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 10, 25, 56, 58, 58, 58, 58, 1, 1, 1, 1, 1] 58
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 35, 20, 21, 22, 23, 24, 25, 37, 36] set([32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057473 none N#CC1=C2C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CNC2=CC=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 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, 48, 48, 19, 19, 7, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 58, 58, 58, 58, 58, 58, 48, 19, 7, 1, 1, 1, 1, 58, 58, 58, 58, 58] 58
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37])
total number of confs: 108
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057473 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057473
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057473/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057473
Building REAL300000057474
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057474'
/scratch/stefan/7769638/working/building/REAL300000057474 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057474

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057474/0 /scratch/stefan/7769638/working/building/REAL300000057474 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 495)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/495
`/scratch/stefan/7769638/working/3D/495' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C(F)C=CC=C23)C=C1)

`REAL300000057474.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057474.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057474/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057474 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C(F)C=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 8, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 48
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057474 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C(F)C=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 23, 24, 25, 26, 27, 28])
total number of confs: 47
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057474 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057474
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057474/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057474
Building REAL300000057475
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057475'
/scratch/stefan/7769638/working/building/REAL300000057475 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057475

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057475/0 /scratch/stefan/7769638/working/building/REAL300000057475 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 496)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/496
`/scratch/stefan/7769638/working/3D/496' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C(C)C=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C)

`REAL300000057475.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057475.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057475/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057475 none COC1=C(C)C=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 5, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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]
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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 32, 32, 32, 101, 119, 119, 109, 111, 119, 119, 119, 119, 1, 1, 2, 2, 2, 2, 2, 2, 1, 9, 32, 101, 119, 119, 119, 119, 2, 2, 2] 119
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 373
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057475 none COC1=C(C)C=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 5, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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]
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, 45, 45, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 119, 119, 119, 119, 119, 119, 119, 119, 119, 45, 18, 7, 1, 1, 1, 1, 119, 119, 119] 119
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40, 41])
total number of confs: 192
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057475 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057475
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057475/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057475
Building REAL300000057476
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057476'
/scratch/stefan/7769638/working/building/REAL300000057476 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057476

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057476/0 /scratch/stefan/7769638/working/building/REAL300000057476 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 497)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/497
`/scratch/stefan/7769638/working/3D/497' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3(C2)OCCO3)C=C1)

`REAL300000057476.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057476.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057476/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057476 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3(C2)OCCO3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 8, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 25
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 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, 35, 36, 37, 38, 39])
total number of confs: 60
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057476 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3(C2)OCCO3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 25
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 40, 41, 22, 23, 24, 25, 26, 27])
total number of confs: 59
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057476 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057476
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057476/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057476
Building REAL300000057477
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057477'
/scratch/stefan/7769638/working/building/REAL300000057477 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057477

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057477/0 /scratch/stefan/7769638/working/building/REAL300000057477 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 498)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/498
`/scratch/stefan/7769638/working/3D/498' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=C(F)C=C(Cl)C=C23)C=C1)

`REAL300000057477.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057477.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057477/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057477 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=C(F)C=C(Cl)C=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
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, 11, 16, 16, 16, 42, 42, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 11, 16, 42, 73, 73, 73, 73, 1, 1] 73
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 24, 25, 26, 27, 36] set([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: 126
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057477 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=C(F)C=C(Cl)C=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 75, 75, 75, 75, 31, 30, 31, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 30, 12, 1, 1, 1, 1, 75, 75] 75
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 197
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057477 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057477
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057477/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057477
Building REAL300000057478
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057478'
/scratch/stefan/7769638/working/building/REAL300000057478 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057478

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057478/0 /scratch/stefan/7769638/working/building/REAL300000057478 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 499)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/499
`/scratch/stefan/7769638/working/3D/499' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=CN=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057478.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057478.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057478/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057478 none CC(CCC1=CC=CN=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 15, 9, 1, 1, 1, 1, 1, 1, 1, 56, 56, 115, 115, 115, 199, 201, 201, 199, 199, 201, 201, 201, 201, 56, 56, 56, 15, 15, 9, 9, 1, 1, 1, 1, 115, 199, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 624
number of broken/clashed sets: 159
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057478 none CC(CCC1=CC=CN=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 108, 130, 201, 201, 201, 201, 201, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 35, 35, 35, 108, 108, 130, 130, 201, 201, 201, 201, 14, 7, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 631
number of broken/clashed sets: 159
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057478 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057478
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057478/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057478
Building REAL300000057479
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057479'
/scratch/stefan/7769638/working/building/REAL300000057479 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057479

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057479/0 /scratch/stefan/7769638/working/building/REAL300000057479 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 500)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/500
`/scratch/stefan/7769638/working/3D/500' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=NC=CN=C23)C=C1)

`REAL300000057479.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057479.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057479/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057479 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=NC=CN=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1] 10
rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 37, 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, 35])
total number of confs: 28
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057479 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=NC=CN=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 10
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 37, 36])
total number of confs: 25
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057479 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057479
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057479/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057479
Building REAL300000057480
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057480'
/scratch/stefan/7769638/working/building/REAL300000057480 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057480

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057480/0 /scratch/stefan/7769638/working/building/REAL300000057480 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 501)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/501
`/scratch/stefan/7769638/working/3D/501' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CN=CC2=CC=CC=C21)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057480.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057480.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057480/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057480 none CC(CCC1=CN=CC2=CC=CC=C21)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 118, 118, 118, 197, 201, 201, 197, 201, 201, 201, 201, 201, 42, 42, 42, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 118, 197, 201, 201, 201, 201] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 3, 36, 38, 39, 37] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46])
total number of confs: 633
number of broken/clashed sets: 144
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057480 none CC(CCC1=CN=CC2=CC=CC=C21)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 36, 119, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 119, 119, 127, 127, 201, 201, 201, 201, 201, 201, 12, 7, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 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, 40, 41, 42])
total number of confs: 558
number of broken/clashed sets: 144
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057480 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057480
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057480/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057480
Building REAL300000057481
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057481'
/scratch/stefan/7769638/working/building/REAL300000057481 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057481

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057481/0 /scratch/stefan/7769638/working/building/REAL300000057481 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 502)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/502
`/scratch/stefan/7769638/working/3D/502' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1=CC=C(CC(C)C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000057481.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057481.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057481/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057481 none CCCC1=CC=C(CC(C)C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 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: [3, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 70, 70, 99, 99, 99, 189, 201, 201, 189, 190, 201, 201, 201, 201, 1, 1, 4, 4, 4, 3, 3, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 70, 99, 189, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 49, 50, 35, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 699
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057481 none CCCC1=CC=C(CC(C)C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 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, 201, 112, 112, 201, 201, 112, 65, 16, 65, 16, 7, 7, 6, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 112, 65, 65, 65, 65, 16, 7, 6, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [48, 45, 46, 15, 16, 17, 18, 19, 20, 23, 24, 47] 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50])
total number of confs: 1376
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057481 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057481
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057481/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057481
Building REAL300000057482
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057482'
/scratch/stefan/7769638/working/building/REAL300000057482 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057482

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057482/0 /scratch/stefan/7769638/working/building/REAL300000057482 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 503)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/503
`/scratch/stefan/7769638/working/3D/503' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2CCC(F)(F)C2)C=C1)

`REAL300000057482.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057482/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057482 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCC(F)(F)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', '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, 11, 8, 8, 1, 5, 5, 5, 5, 15, 15, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 1, 1, 1, 1, 9, 13, 13, 13, 23, 23, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 9, 13, 23, 52, 52, 52, 52, 52, 52, 52, 1, 1] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 20, 21, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057482 none O=C([O-])C1=CC=C(NC(=O)NN=CC2CCC(F)(F)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', '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, 11, 8, 8, 1, 5, 5, 5, 5, 15, 15, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 57, 57, 57, 57, 30, 29, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 29, 12, 1, 1, 1, 1, 1, 1, 1, 57, 57] 57
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 153
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057482 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057482
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057482/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057482
Building REAL300000057483
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057483'
/scratch/stefan/7769638/working/building/REAL300000057483 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057483

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057483/0 /scratch/stefan/7769638/working/building/REAL300000057483 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 504)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/504
`/scratch/stefan/7769638/working/3D/504' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C=CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1C)

`REAL300000057483.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057483.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057483/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057483 none CCOC(=O)C=CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 44, 40, 10, 40, 10, 1, 1, 1, 1, 1, 1, 8, 8, 12, 13, 13, 29, 37, 37, 29, 29, 37, 37, 37, 37, 1, 1, 73, 73, 73, 73, 73, 10, 10, 1, 1, 8, 12, 29, 37, 37, 37, 37, 2, 2, 2] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 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, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 407
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057483 none CCOC(=O)C=CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 195, 195, 109, 195, 109, 37, 37, 37, 37, 10, 10, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 201, 201, 201, 201, 201, 109, 109, 37, 37, 10, 6, 6, 1, 1, 1, 1, 37, 37, 37] 201
rigid atoms, others: [40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46])
total number of confs: 564
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057483 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057483
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057483/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057483
Building REAL300000057484
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057484'
/scratch/stefan/7769638/working/building/REAL300000057484 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057484

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057484/0 /scratch/stefan/7769638/working/building/REAL300000057484 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 505)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/505
`/scratch/stefan/7769638/working/3D/505' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CC4=CC=CC2=C43)C=C1)

`REAL300000057484.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057484.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057484/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057484 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CC4=CC=CC2=C43)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 15, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 8, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 60
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057484 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CC4=CC=CC2=C43)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 22, 23, 22, 23, 23, 22, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 22, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 23
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 41, 25, 26, 27, 28, 29, 30])
total number of confs: 66
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057484 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057484
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057484/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057484
Building REAL300000057485
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057485'
/scratch/stefan/7769638/working/building/REAL300000057485 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057485

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057485/0 /scratch/stefan/7769638/working/building/REAL300000057485 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 506)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/506
`/scratch/stefan/7769638/working/3D/506' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3CCSCC23)C=C1)

`REAL300000057485.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057485/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057485 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3CCSCC23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 10, 5, 5, 14, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 8, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 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, 35, 36, 37, 38, 39, 40])
total number of confs: 47
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057485 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN3CCSCC23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 10, 5, 5, 14, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 20
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 41, 22, 23, 24, 25, 26, 27])
total number of confs: 49
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057485 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057485
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057485/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057485
Building REAL300000057486
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057486'
/scratch/stefan/7769638/working/building/REAL300000057486 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057486

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057486/0 /scratch/stefan/7769638/working/building/REAL300000057486 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 507)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/507
`/scratch/stefan/7769638/working/3D/507' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C3=CC=CC=C3OCC2F)C=C1)

`REAL300000057486.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057486.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057486/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057486 none O=C([O-])C1=CC=C(NC(=O)NN=C2C3=CC=CC=C3OCC2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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, 9, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 17, 17, 17, 1, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25, 26, 37, 36] set([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: 38
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057486 none O=C([O-])C1=CC=C(NC(=O)NN=C2C3=CC=CC=C3OCC2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 17, 17] 17
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 37, 36])
total number of confs: 41
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057486 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057486
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057486/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057486
Building REAL300000057487
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057487'
/scratch/stefan/7769638/working/building/REAL300000057487 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057487

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057487/0 /scratch/stefan/7769638/working/building/REAL300000057487 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 508)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/508
`/scratch/stefan/7769638/working/3D/508' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCCO3)N=N2)C=C1)

`REAL300000057487.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057487.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057487/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057487 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCCO3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 10, 14, 14, 14, 35, 35, 49, 49, 49, 139, 201, 201, 201, 201, 49, 49, 1, 1, 1, 1, 10, 14, 35, 49, 139, 139, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 665
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057487 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCCO3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 49, 49, 39, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 1, 1, 49, 49, 49, 49, 39, 19, 7, 1, 8, 8, 27, 27, 27, 27, 27, 27, 27, 49, 49] 201
rigid atoms, others: [12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057487 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCCO3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 196, 106, 106, 106, 65, 65, 27, 27, 27, 7, 1, 1, 1, 1, 1, 1, 27, 27, 201, 201, 201, 201, 196, 106, 65, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42])
total number of confs: 584
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057487 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057487
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057487/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057487
Building REAL300000057488
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057488'
/scratch/stefan/7769638/working/building/REAL300000057488 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057488

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057488/0 /scratch/stefan/7769638/working/building/REAL300000057488 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 509)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/509
`/scratch/stefan/7769638/working/3D/509' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1)

`REAL300000057488.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057488.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057488/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057488 none CCCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [19, 9, 1, 1, 1, 1, 1, 8, 8, 28, 28, 28, 73, 87, 87, 73, 73, 87, 87, 87, 87, 1, 1, 19, 19, 19, 19, 19, 9, 9, 1, 8, 28, 73, 87, 87, 87, 87] 169
rigid atoms, others: [2, 3, 4, 5, 6, 21, 22, 30] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 389
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057488 none CCCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [169, 162, 87, 87, 87, 49, 49, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 87, 87, 169, 169, 169, 169, 169, 162, 162, 87, 49, 16, 7, 1, 1, 1, 1] 169
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 567
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057488 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057488
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057488/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057488
Building REAL300000057489
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057489'
/scratch/stefan/7769638/working/building/REAL300000057489 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057489

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057489/0 /scratch/stefan/7769638/working/building/REAL300000057489 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 510)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/510
`/scratch/stefan/7769638/working/3D/510' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C=CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C)

`REAL300000057489.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057489.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057489/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057489 none CC1=CC(C)=C(C=CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 7, 7, 33, 33, 63, 65, 63, 110, 110, 110, 110, 110, 110, 110, 110, 110, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 7, 7, 33, 65, 110, 110, 110, 110, 110, 1, 2, 2, 2] 110
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 23, 24, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45])
total number of confs: 343
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057489 none CC1=CC(C)=C(C=CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [107, 108, 110, 110, 110, 86, 86, 42, 42, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 86, 86, 42, 14, 7, 1, 1, 1, 1, 110, 110, 110, 110] 110
rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 279
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057489 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057489
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057489/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057489
Building REAL300000057490
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057490'
/scratch/stefan/7769638/working/building/REAL300000057490 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057490

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057490/0 /scratch/stefan/7769638/working/building/REAL300000057490 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 511)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/511
`/scratch/stefan/7769638/working/3D/511' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC(F)=CC=C2F)=N1)

`REAL300000057490.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057490/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057490 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC(F)=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 41, 41, 41, 94, 104, 104, 101, 101, 104, 104, 104, 104, 1, 1, 11, 11, 11, 9, 11, 11, 11, 1, 2, 2, 2, 1, 11, 41, 94, 104, 104, 104, 104, 11, 9, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 32, 19, 20, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 323
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057490 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC(F)=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 37, 37, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 104, 104, 201, 201, 201, 201, 201, 201, 201, 104, 104, 104, 104, 104, 37, 12, 7, 1, 1, 1, 1, 201, 201, 201] 201
rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057490 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC(F)=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 11, 41, 41, 105, 105, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 41, 105, 201, 201, 201, 201, 201, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 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])
total number of confs: 578
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057490 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057490
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057490/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057490
Building REAL300000057491
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057491'
/scratch/stefan/7769638/working/building/REAL300000057491 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057491

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057491/0 /scratch/stefan/7769638/working/building/REAL300000057491 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 512)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/512
`/scratch/stefan/7769638/working/3D/512' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2CCC2)C=C1)

`REAL300000057491.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057491.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057491/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057491 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 39, 39, 25, 25, 88, 88, 88, 39, 39, 21, 21, 21, 13, 7, 1, 1, 1, 1, 39, 39, 88, 88, 88, 88, 88, 88, 88, 39, 39] 88
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 280
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057491 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [6, 1, 6, 6, 21, 21, 21, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 6, 6, 6, 21, 39, 39, 39, 39, 39, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1] 88
rigid atoms, others: [1, 35, 36, 44, 45, 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, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 115
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057491 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [23, 2, 23, 23, 50, 50, 50, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 21, 22, 22, 50, 88, 88, 88, 88, 88, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8] 88
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 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, 44, 45])
total number of confs: 256
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057491 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057491
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057491/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057491
Building REAL300000057492
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057492'
/scratch/stefan/7769638/working/building/REAL300000057492 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057492

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057492/0 /scratch/stefan/7769638/working/building/REAL300000057492 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 513)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/513
`/scratch/stefan/7769638/working/3D/513' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=CC(F)=C3N=C2)C=C1)

`REAL300000057492.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057492.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057492/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057492 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=CC(F)=C3N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 7, 7, 3, 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, 4, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 4, 5, 5, 9, 9, 9, 9, 9, 1, 1] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37, 36] set([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: 21
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057492 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=CC(F)=C3N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 21, 20, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 20, 6, 1, 1, 1, 1, 1, 45, 45] 45
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 37, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 125
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057492 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057492
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057492/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057492
Building REAL300000057493
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057493'
/scratch/stefan/7769638/working/building/REAL300000057493 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057493

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057493/0 /scratch/stefan/7769638/working/building/REAL300000057493 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 514)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/514
`/scratch/stefan/7769638/working/3D/514' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C(F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057493.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057493/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057493 none CN(C)C1=CC=C(F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 1, 1, 1, 5, 12, 25, 25, 25, 25, 25] 25
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 33, 31] set([0, 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])
total number of confs: 73
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057493 none CN(C)C1=CC=C(F)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 24, 25, 25, 25, 24, 24, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 15, 7, 1, 1, 1, 1] 25
rigid atoms, others: [37, 38, 39, 40, 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, 36])
total number of confs: 63
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057493 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057493
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057493/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057493
Building REAL300000057494
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057494'
/scratch/stefan/7769638/working/building/REAL300000057494 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057494

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057494/0 /scratch/stefan/7769638/working/building/REAL300000057494 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 515)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/515
`/scratch/stefan/7769638/working/3D/515' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=C1)CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057494.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057494.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057494/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057494 none COC1=CC=C2C(=C1)CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 32, 32, 26, 27, 32, 32, 32, 32, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 26, 32, 32, 32, 32] 32
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 33, 28, 29, 30, 31] set([0, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40])
total number of confs: 120
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057494 none COC1=CC=C2C(=C1)CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 32, 32, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 7, 1, 1, 1, 1] 32
rigid atoms, others: [37, 38, 39, 40, 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, 36])
total number of confs: 74
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057494 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057494
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057494/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057494
Building REAL300000057495
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057495'
/scratch/stefan/7769638/working/building/REAL300000057495 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057495

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057495/0 /scratch/stefan/7769638/working/building/REAL300000057495 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 516)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/516
`/scratch/stefan/7769638/working/3D/516' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=CSC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057495.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057495.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057495/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057495 none CC(C)(C)C1=CSC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 61, 68, 68, 61, 61, 68, 68, 68, 68, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 7, 26, 61, 68, 68, 68, 68] 75
rigid atoms, others: [1, 4, 5, 6, 33, 8, 7, 23] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 247
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057495 none CC(C)(C)C1=CSC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 68, 75, 75, 68, 68, 68, 43, 43, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 68, 75, 75, 75, 75, 75, 75, 75, 75, 75, 68, 43, 14, 7, 1, 1, 1, 1] 75
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])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057495 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057495
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057495/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057495
Building REAL300000057496
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057496'
/scratch/stefan/7769638/working/building/REAL300000057496 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057496

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057496/0 /scratch/stefan/7769638/working/building/REAL300000057496 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 517)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/517
`/scratch/stefan/7769638/working/3D/517' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C=CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1)

`REAL300000057496.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057496.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057496/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057496 none CC1=CC(C)=C(C=CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 4, 4, 12, 12, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 4, 12, 26, 48, 48, 48, 48, 48, 2, 2, 2, 1] 48
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 45, 23, 24, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057496 none CC1=CC(C)=C(C=CC=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 26, 14, 7, 1, 1, 1, 1, 48, 48, 48, 48] 48
rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 118
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057496 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057496
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057496/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057496
Building REAL300000057497
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057497'
/scratch/stefan/7769638/working/building/REAL300000057497 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057497

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057497/0 /scratch/stefan/7769638/working/building/REAL300000057497 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 518)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/518
`/scratch/stefan/7769638/working/3D/518' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057497.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057497.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057497/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057497 none COCCC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 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: [48, 14, 7, 1, 1, 1, 1, 1, 1, 8, 8, 28, 29, 29, 59, 69, 69, 59, 67, 69, 69, 69, 69, 1, 49, 49, 49, 14, 14, 7, 7, 1, 8, 28, 59, 69, 69, 69, 69] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057497 none COCCC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 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, 165, 69, 69, 69, 69, 28, 28, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 69, 201, 201, 201, 201, 201, 165, 165, 69, 28, 10, 7, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 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])
total number of confs: 744
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057497 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057497
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057497/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057497
Building REAL300000057498
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057498'
/scratch/stefan/7769638/working/building/REAL300000057498 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057498

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057498/0 /scratch/stefan/7769638/working/building/REAL300000057498 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 519)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/519
`/scratch/stefan/7769638/working/3D/519' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CC3)C=N2)C=C1)

`REAL300000057498.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057498.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057498/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057498 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CC3)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 14, 14, 14, 37, 37, 50, 50, 50, 80, 80, 50, 50, 1, 1, 1, 1, 10, 14, 37, 50, 80, 80, 80, 80, 80, 50, 1, 1] 80
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 201
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057498 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CC3)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [55, 53, 55, 51, 55, 55, 47, 22, 22, 22, 8, 8, 1, 1, 1, 1, 1, 9, 9, 1, 1, 55, 55, 55, 55, 47, 22, 8, 1, 9, 9, 9, 9, 9, 1, 55, 55] 87
rigid atoms, others: [34, 12, 13, 14, 15, 16, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057498 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CC3)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 87, 87, 87, 87, 86, 47, 47, 47, 23, 23, 9, 9, 9, 1, 1, 1, 1, 9, 9, 87, 87, 87, 87, 86, 47, 23, 9, 1, 1, 1, 1, 1, 9, 87, 87] 87
rigid atoms, others: [32, 33, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 232
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057498 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057498
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057498/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057498
Building REAL300000057499
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057499'
/scratch/stefan/7769638/working/building/REAL300000057499 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057499

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057499/0 /scratch/stefan/7769638/working/building/REAL300000057499 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 520)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/520
`/scratch/stefan/7769638/working/3D/520' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Br)=CC(F)=C2[O-])C=C1)

`REAL300000057499.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057499.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057499/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057499 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Br)=CC(F)=C2[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', '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, 11, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 6, 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, 7, 3, 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, 8, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 8, 11, 14, 14, 14, 1, 1] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 34
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057499 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Br)=CC(F)=C2[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', '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, 11, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 6, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 25, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 25, 8, 4, 1, 1, 26, 26] 26
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 69
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057499 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057499/1 /scratch/stefan/7769638/working/building/REAL300000057499 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 521)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/521
`/scratch/stefan/7769638/working/3D/521' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Br)=CC(F)=C2O)C=C1)

`REAL300000057499.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057499.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057499/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057499 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Br)=CC(F)=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 13, 13, 13, 22, 22, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 9, 13, 22, 26, 26, 52, 1, 1] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 103
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057499 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Br)=CC(F)=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 15, 10, 1, 1, 2, 27, 27] 54
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33])
total number of confs: 73
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057499 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057499
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057499/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057499/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057499
Building REAL300000057500
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057500'
/scratch/stefan/7769638/working/building/REAL300000057500 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057500

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057500/0 /scratch/stefan/7769638/working/building/REAL300000057500 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 522)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/522
`/scratch/stefan/7769638/working/3D/522' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC(F)=C2O)C=C1)

`REAL300000057500.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057500.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057500/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057500 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC(F)=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 22, 22, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 10, 13, 22, 26, 26, 52, 1, 1] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 101
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057500 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC(F)=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 15, 10, 1, 1, 2, 27, 27] 54
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33])
total number of confs: 73
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057500 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057500/1 /scratch/stefan/7769638/working/building/REAL300000057500 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 523)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/523
`/scratch/stefan/7769638/working/3D/523' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC(F)=C2[O-])C=C1)

`REAL300000057500.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057500.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057500/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057500 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC(F)=C2[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', '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, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 6, 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, 7, 3, 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, 9, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 9, 11, 14, 14, 14, 1, 1] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 32
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057500 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC(F)=C2[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', '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, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 6, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 25, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 25, 8, 4, 1, 1, 26, 26] 26
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 69
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057500 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057500
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057500/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057500/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057500
Building REAL300000057501
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057501'
/scratch/stefan/7769638/working/building/REAL300000057501 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057501

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057501/0 /scratch/stefan/7769638/working/building/REAL300000057501 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 524)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/524
`/scratch/stefan/7769638/working/3D/524' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCCCC1)

`REAL300000057501.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057501.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057501/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057501 none C=CCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCCCC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 44, 45, 45, 111, 127, 127, 111, 116, 127, 127, 127, 127, 1, 1, 1, 1, 1, 23, 23, 23, 9, 9, 7, 44, 111, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 491
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057501 none C=CCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCCCC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 46, 46, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 201, 201, 201, 201, 201, 46, 16, 7, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127] 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, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 664
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057501 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057501
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057501/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057501
Building REAL300000057502
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057502'
/scratch/stefan/7769638/working/building/REAL300000057502 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057502

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057502/0 /scratch/stefan/7769638/working/building/REAL300000057502 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 525)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/525
`/scratch/stefan/7769638/working/3D/525' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC2=C1CCCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057502.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057502.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057502/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057502 none CN1N=CC2=C1CCCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 1, 1, 7, 8, 8, 23, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 24, 24, 24, 24] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057502 none CN1N=CC2=C1CCCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 24, 24, 24, 24, 24, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 7, 1, 1, 1, 1] 24
rigid atoms, others: [39, 40, 41, 42, 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, 36, 37, 38])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057502 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057502
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057502/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057502
Building REAL300000057503
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057503'
/scratch/stefan/7769638/working/building/REAL300000057503 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057503

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057503/0 /scratch/stefan/7769638/working/building/REAL300000057503 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 526)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/526
`/scratch/stefan/7769638/working/3D/526' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C=C1C)

`REAL300000057503.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057503.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057503/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057503 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 52, 52, 26, 40, 52, 52, 52, 26, 26, 26, 15, 7, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52] 52
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 183
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057503 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 29, 29, 29, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 52, 52, 52, 52, 52, 1, 1, 1, 2, 2, 2] 52
rigid atoms, others: [1, 34, 35, 33, 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, 36, 37, 38])
total number of confs: 145
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057503 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057503
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057503/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057503
Building REAL300000057504
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057504'
/scratch/stefan/7769638/working/building/REAL300000057504 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057504

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057504/0 /scratch/stefan/7769638/working/building/REAL300000057504 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 527)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/527
`/scratch/stefan/7769638/working/3D/527' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C2C=NN3CCO)C=C1)

`REAL300000057504.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057504.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057504/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057504 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C2C=NN3CCO)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 8, 8, 5, 5, 12, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 29, 29, 1, 1, 1, 1, 8, 12, 17, 17, 17, 17, 17, 17, 17, 29, 29, 29, 29, 87, 1, 1] 87
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 187
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057504 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C2C=NN3CCO)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 8, 8, 5, 5, 12, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 16, 17, 17, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 17, 17, 17, 17, 14, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 27, 17, 17] 87
rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 112
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057504 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057504
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057504/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057504
Building REAL300000057505
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057505'
/scratch/stefan/7769638/working/building/REAL300000057505 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057505

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057505/0 /scratch/stefan/7769638/working/building/REAL300000057505 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 528)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/528
`/scratch/stefan/7769638/working/3D/528' -> `0.mol2'
Preparing input files

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

`REAL300000057505.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057505.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057505/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057505 none CC(CS(=O)(=O)N(C)C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 5, 14, 11, 11, 8, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 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]
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: [23, 23, 23, 48, 76, 76, 76, 76, 76, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 48, 48, 76, 76, 76, 76, 76, 76, 6, 6, 1, 1, 1, 1] 76
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 287
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057505 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057505
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057505/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057505
Building REAL300000057506
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057506'
/scratch/stefan/7769638/working/building/REAL300000057506 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057506

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057506/0 /scratch/stefan/7769638/working/building/REAL300000057506 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 529)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/529
`/scratch/stefan/7769638/working/3D/529' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(Cl)C=CS1)

`REAL300000057506.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057506.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057506/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057506 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(Cl)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 14, 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, 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
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [53, 34, 34, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 90, 90, 90, 90, 90, 53, 53, 53, 53, 53, 15, 7, 1, 1, 1, 1, 90, 90] 102
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 254
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057506 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(Cl)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 14, 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, 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
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [28, 9, 1, 9, 9, 44, 44, 44, 80, 90, 90, 80, 81, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 27, 43, 80, 90, 90, 90, 90, 1, 1] 102
rigid atoms, others: [2, 35, 34, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 385
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057506 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057506
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057506/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057506
Building REAL300000057507
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057507'
/scratch/stefan/7769638/working/building/REAL300000057507 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057507

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057507/0 /scratch/stefan/7769638/working/building/REAL300000057507 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 530)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/530
`/scratch/stefan/7769638/working/3D/530' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC(F)=C(F)C(F)=C23)C=C1)

`REAL300000057507.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057507.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057507/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057507 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC(F)=C(F)C(F)=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 36, 36, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 8, 12, 36, 51, 51, 51, 1, 1] 51
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 25, 26, 27, 28, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34])
total number of confs: 86
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057507 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC(F)=C(F)C(F)=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
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, 25, 24, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 24, 10, 1, 1, 1, 59, 59] 59
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 36, 35, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 157
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057507 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057507
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057507/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057507
Building REAL300000057508
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057508'
/scratch/stefan/7769638/working/building/REAL300000057508 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057508

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057508/0 /scratch/stefan/7769638/working/building/REAL300000057508 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 531)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/531
`/scratch/stefan/7769638/working/3D/531' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=C(F)C=C(F)C(F)=C23)C=C1)

`REAL300000057508.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057508.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057508/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057508 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=C(F)C=C(F)C(F)=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
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, 8, 12, 12, 12, 36, 36, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 8, 12, 36, 47, 47, 47, 1, 1] 47
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 25, 26, 27, 28, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34])
total number of confs: 82
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057508 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=C(F)C=C(F)C(F)=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
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, 53, 54, 53, 54, 54, 53, 22, 22, 22, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 53, 22, 10, 1, 1, 1, 54, 54] 54
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 36, 35, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 144
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057508 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057508
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057508/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057508
Building REAL300000057509
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057509'
/scratch/stefan/7769638/working/building/REAL300000057509 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057509

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057509/0 /scratch/stefan/7769638/working/building/REAL300000057509 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 532)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/532
`/scratch/stefan/7769638/working/3D/532' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1O)

`REAL300000057509.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057509.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057509/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057509 none COC1=CC(C)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 37, 41, 41, 38, 38, 41, 41, 41, 41, 1, 1, 4, 4, 4, 1, 2, 2, 2, 1, 7, 14, 37, 41, 41, 41, 41, 2] 82
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 142
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057509 none COC1=CC(C)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 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, 41, 41, 41, 41, 41, 41, 27, 27, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 27, 15, 7, 1, 1, 1, 1, 82] 82
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 163
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057509 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057509
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057509/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057509
Building REAL300000057510
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057510'
/scratch/stefan/7769638/working/building/REAL300000057510 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057510

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057510/0 /scratch/stefan/7769638/working/building/REAL300000057510 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 533)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/533
`/scratch/stefan/7769638/working/3D/533' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057510.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057510/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057510 none CC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1] 26
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 41, 39, 40, 20, 21, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24])
total number of confs: 67
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057510 none CC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 26, 26, 26, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 7, 1, 1, 1, 1, 26, 26, 26, 26] 26
rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 58
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057510 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057510
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057510/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057510
Building REAL300000057511
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057511'
/scratch/stefan/7769638/working/building/REAL300000057511 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057511

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057511/0 /scratch/stefan/7769638/working/building/REAL300000057511 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 534)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/534
`/scratch/stefan/7769638/working/3D/534' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCOCC1=CC=CC=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057511.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057511.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057511/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057511 none CC(CCOCC1=CC=CC=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 53, 33, 13, 3, 1, 1, 1, 1, 1, 1, 1, 82, 82, 140, 140, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 82, 82, 53, 53, 33, 33, 3, 3, 1, 1, 1, 1, 1, 140, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45])
total number of confs: 763
number of broken/clashed sets: 195
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057511 none CC(CCOCC1=CC=CC=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 52, 70, 108, 201, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 52, 52, 70, 70, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 788
number of broken/clashed sets: 195
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057511 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057511
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057511/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057511
Building REAL300000057512
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057512'
/scratch/stefan/7769638/working/building/REAL300000057512 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057512

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057512/0 /scratch/stefan/7769638/working/building/REAL300000057512 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 535)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/535
`/scratch/stefan/7769638/working/3D/535' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+]1CCC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057512.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057512.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057512/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057512 none C[NH+]1CCC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 12, 12, 28, 29, 29, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 12, 28, 40, 40, 40, 40, 40, 1, 1, 1, 1] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 41, 40, 21, 22, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057512 none C[NH+]1CCC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 18, 18, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 18, 10, 7, 1, 1, 1, 1, 40, 40, 40, 40] 40
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057512 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057512
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057512/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057512
Building REAL300000057513
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057513'
/scratch/stefan/7769638/working/building/REAL300000057513 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057513

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057513/0 /scratch/stefan/7769638/working/building/REAL300000057513 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 536)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/536
`/scratch/stefan/7769638/working/3D/536' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(CCCC3)N2)C=C1)

`REAL300000057513.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057513/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057513 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(CCCC3)N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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, 1, 8, 8, 8, 8, 24, 24, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 8, 8, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1] 31
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 52
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057513 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(CCCC3)N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 33
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 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, 40, 22, 23, 24, 25, 26, 27, 28, 39])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057513 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057513
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057513/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057513
Building REAL300000057514
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057514'
/scratch/stefan/7769638/working/building/REAL300000057514 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057514

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057514/0 /scratch/stefan/7769638/working/building/REAL300000057514 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 537)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/537
`/scratch/stefan/7769638/working/3D/537' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1=CC=C([N+](=O)[O-])C=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057514.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057514.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057514/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057514 none CSC1=CC=C([N+](=O)[O-])C=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 14, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 55, 57, 57, 55, 57, 57, 57, 57, 57, 7, 7, 7, 1, 1, 1, 7, 7, 7, 25, 55, 57, 57, 57, 57] 85
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 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: 172
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057514 none CSC1=CC=C([N+](=O)[O-])C=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 14, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 57, 57, 57, 47, 57, 57, 57, 57, 57, 34, 34, 34, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 85, 85, 85, 57, 57, 57, 34, 34, 34, 12, 7, 1, 1, 1, 1] 85
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])
total number of confs: 204
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057514 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057514
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057514/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057514
Building REAL300000057515
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057515'
/scratch/stefan/7769638/working/building/REAL300000057515 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057515

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057515/0 /scratch/stefan/7769638/working/building/REAL300000057515 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 538)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/538
`/scratch/stefan/7769638/working/3D/538' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC1CCCCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057515.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057515.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057515/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057515 none CCC(CC1CCCCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 33, 10, 1, 1, 1, 1, 1, 1, 1, 33, 33, 92, 92, 92, 169, 186, 186, 169, 169, 186, 186, 186, 186, 65, 65, 65, 65, 65, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 169, 186, 186, 186, 186] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 41, 36, 38, 37, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45, 46, 47])
total number of confs: 812
number of broken/clashed sets: 114
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057515 none CCC(CC1CCCCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [81, 42, 42, 42, 146, 185, 186, 186, 186, 185, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 81, 81, 81, 81, 81, 146, 146, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 18, 7, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 14, 15, 16, 17, 18, 19, 46, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 832
number of broken/clashed sets: 114
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057515 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057515
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057515/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057515
Building REAL300000057516
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057516'
/scratch/stefan/7769638/working/building/REAL300000057516 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057516

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057516/0 /scratch/stefan/7769638/working/building/REAL300000057516 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 539)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/539
`/scratch/stefan/7769638/working/3D/539' -> `0.mol2'
Preparing input files

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

`REAL300000057516.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057516.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057516/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057516 none CCC(CCC(F)(F)F)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 1, 5, 5, 5, 15, 15, 15, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [81, 48, 48, 48, 139, 153, 157, 157, 157, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 139, 139, 157, 157, 16, 7, 1, 1, 1, 1] 169
rigid atoms, others: [34, 35, 36, 37, 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])
total number of confs: 772
number of broken/clashed sets: 85
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057516 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057516
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057516/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057516
Building REAL300000057517
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057517'
/scratch/stefan/7769638/working/building/REAL300000057517 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057517

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057517/0 /scratch/stefan/7769638/working/building/REAL300000057517 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 540)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/540
`/scratch/stefan/7769638/working/3D/540' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCOC1)

`REAL300000057517.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057517.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057517/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057517 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 12, 5, 7, 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, 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, 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: [48, 34, 34, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 60, 60, 60, 60, 60, 48, 48, 48, 48, 48, 12, 7, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60] 77
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 219
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057517 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 12, 5, 7, 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, 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, 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: [26, 11, 1, 11, 11, 37, 37, 37, 56, 60, 60, 56, 56, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 37, 56, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 1, 1] 77
rigid atoms, others: [2, 35, 36, 37, 38, 39, 40, 41, 42, 34, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 270
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057517 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057517
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057517/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057517
Building REAL300000057518
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057518'
/scratch/stefan/7769638/working/building/REAL300000057518 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057518

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057518/0 /scratch/stefan/7769638/working/building/REAL300000057518 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 541)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/541
`/scratch/stefan/7769638/working/3D/541' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057518.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057518/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057518 none CC1(C)CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 17] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 37, 35, 36, 33, 38, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41, 42, 43, 44])
total number of confs: 57
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057518 none CC1(C)CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 13, 7, 1, 1, 1, 1] 17
rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 45
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057518 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057518
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057518/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057518
Building REAL300000057519
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057519'
/scratch/stefan/7769638/working/building/REAL300000057519 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057519

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057519/0 /scratch/stefan/7769638/working/building/REAL300000057519 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 542)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/542
`/scratch/stefan/7769638/working/3D/542' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC3=CC=CC=C3C2)C=C1)

`REAL300000057519.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057519.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057519/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057519 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC3=CC=CC=C3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 10, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1] 31
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 58
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057519 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC3=CC=CC=C3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 31
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 44, 45, 24, 25, 26, 27, 28, 29])
total number of confs: 79
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057519 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057519
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057519/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057519
Building REAL300000057520
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057520'
/scratch/stefan/7769638/working/building/REAL300000057520 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057520

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057520/0 /scratch/stefan/7769638/working/building/REAL300000057520 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 543)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/543
`/scratch/stefan/7769638/working/3D/543' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(C3OCCO3)=CS2)C=C1)

`REAL300000057520.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057520.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057520/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057520 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(C3OCCO3)=CS2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 5, 12, 5, 5, 12, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 47, 47, 91, 91, 91, 153, 153, 153, 153, 91, 91, 1, 1, 1, 1, 8, 12, 47, 153, 153, 153, 153, 153, 91, 1, 1] 153
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: 349
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057520 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(C3OCCO3)=CS2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 5, 12, 5, 5, 12, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 91, 87, 91, 91, 85, 36, 36, 36, 8, 8, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 91, 91, 91, 91, 85, 35, 8, 13, 13, 13, 13, 13, 1, 91, 91] 152
rigid atoms, others: [35, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 288
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057520 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(C3OCCO3)=CS2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 5, 12, 5, 5, 12, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [152, 152, 152, 152, 152, 152, 152, 101, 101, 101, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 152, 152, 152, 152, 152, 101, 59, 1, 1, 1, 1, 1, 13, 152, 152] 152
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 442
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057520 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057520
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057520/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057520
Building REAL300000057521
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057521'
/scratch/stefan/7769638/working/building/REAL300000057521 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057521

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057521/0 /scratch/stefan/7769638/working/building/REAL300000057521 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 544)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/544
`/scratch/stefan/7769638/working/3D/544' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCOCC1)

`REAL300000057521.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057521.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057521/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057521 none C=CCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCOCC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 10, 1, 1, 1, 9, 9, 41, 42, 42, 107, 129, 129, 107, 107, 129, 129, 129, 129, 1, 1, 1, 1, 1, 23, 23, 23, 10, 10, 9, 41, 107, 129, 129, 129, 129, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 551
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057521 none C=CCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCOCC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 129, 52, 52, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 129, 129, 129, 129, 129, 201, 201, 201, 201, 201, 52, 16, 7, 1, 1, 1, 1, 129, 129, 129, 129, 129, 129, 129, 129] 201
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 660
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057521 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057521
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057521/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057521
Building REAL300000057522
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057522'
/scratch/stefan/7769638/working/building/REAL300000057522 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057522

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057522/0 /scratch/stefan/7769638/working/building/REAL300000057522 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 545)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/545
`/scratch/stefan/7769638/working/3D/545' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCC(CC1=CC=C(F)C=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057522.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057522.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057522/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057522 none CC(C)OCC(CC1=CC=C(F)C=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [134, 104, 134, 50, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 31, 31, 31, 78, 100, 100, 78, 91, 100, 100, 100, 100, 134, 134, 134, 134, 134, 134, 134, 50, 50, 3, 3, 1, 1, 1, 1, 31, 78, 100, 100, 100, 100] 201
rigid atoms, others: [11, 6, 39, 8, 9, 10, 7, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48])
total number of confs: 820
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057522 none CC(C)OCC(CC1=CC=C(F)C=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 91, 103, 63, 17, 17, 17, 73, 100, 100, 73, 97, 100, 100, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 103, 103, 103, 103, 103, 103, 103, 63, 63, 73, 73, 100, 100, 100, 100, 8, 6, 1, 1, 1, 1] 201
rigid atoms, others: [45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 732
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057522 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057522
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057522/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057522
Building REAL300000057523
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057523'
/scratch/stefan/7769638/working/building/REAL300000057523 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057523

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057523/0 /scratch/stefan/7769638/working/building/REAL300000057523 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 546)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/546
`/scratch/stefan/7769638/working/3D/546' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2NC(=O)C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1OC)

`REAL300000057523.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057523.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057523/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057523 none COC1=CC=C2NC(=O)C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 28, 31, 31, 29, 29, 31, 31, 31, 31, 1, 1, 1, 6, 3, 3, 3, 1, 1, 1, 7, 28, 31, 31, 31, 31, 7, 7, 7] 49
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 33, 26, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 104
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057523 none COC1=CC=C2NC(=O)C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 6, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 31, 31, 31, 49, 49, 49, 49, 31, 31, 31, 17, 6, 1, 1, 1, 1, 49, 49, 49] 49
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 141
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057523 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057523
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057523/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057523
Building REAL300000057524
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057524'
/scratch/stefan/7769638/working/building/REAL300000057524 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057524

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057524/0 /scratch/stefan/7769638/working/building/REAL300000057524 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 547)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/547
`/scratch/stefan/7769638/working/3D/547' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C2CCSCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057524.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057524.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057524/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057524 none CN1N=C2CCSCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 14, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 10, 10, 31, 32, 32, 52, 54, 54, 52, 54, 54, 54, 54, 54, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 31, 52, 54, 54, 54, 54] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057524 none CN1N=C2CCSCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 14, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 35, 35, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 35, 14, 7, 1, 1, 1, 1] 54
rigid atoms, others: [37, 38, 39, 40, 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, 36])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057524 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057524
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057524/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057524
Building REAL300000057525
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057525'
/scratch/stefan/7769638/working/building/REAL300000057525 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057525

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057525/0 /scratch/stefan/7769638/working/building/REAL300000057525 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 548)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/548
`/scratch/stefan/7769638/working/3D/548' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(C)(C)CC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057525.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057525.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057525/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057525 none CC1CCC(C)(C)CC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 9, 28, 29, 29, 28, 28, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 9, 28, 29, 29, 29, 29] 29
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 10, 9, 26, 27, 28, 29, 30, 37] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 98
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057525 none CC1CCC(C)(C)CC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 7, 1, 1, 1, 1] 29
rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 68
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057525 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057525
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057525/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057525
Building REAL300000057526
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057526'
/scratch/stefan/7769638/working/building/REAL300000057526 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057526

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057526/0 /scratch/stefan/7769638/working/building/REAL300000057526 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 549)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/549
`/scratch/stefan/7769638/working/3D/549' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1)

`REAL300000057526.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057526/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057526 none CCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [8, 1, 1, 1, 1, 1, 13, 13, 39, 39, 39, 99, 127, 127, 99, 111, 127, 127, 127, 127, 1, 1, 6, 6, 2, 6, 6, 1, 8, 8, 8, 8, 8, 1, 13, 39, 99, 127, 127, 127, 127, 6, 6, 4, 6, 6] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 514
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057526 none CCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [189, 127, 127, 127, 55, 55, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 127, 127, 198, 198, 180, 198, 198, 127, 189, 189, 189, 189, 189, 127, 55, 17, 7, 1, 1, 1, 1, 198, 198, 198, 198, 198] 201
rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45])
total number of confs: 784
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057526 none CCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [19, 6, 6, 6, 6, 6, 33, 33, 81, 81, 81, 171, 198, 198, 171, 186, 198, 198, 198, 198, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 19, 6, 33, 81, 171, 198, 198, 198, 198, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 720
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057526 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057526
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057526/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057526
Building REAL300000057527
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057527'
/scratch/stefan/7769638/working/building/REAL300000057527 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057527

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057527/0 /scratch/stefan/7769638/working/building/REAL300000057527 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 550)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/550
`/scratch/stefan/7769638/working/3D/550' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C[C@@H]3CC[C@@H](C3)C2)C=C1)

`REAL300000057527.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057527.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057527/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057527 none O=C([O-])C1=CC=C(NC(=O)NN=C2C[C@@H]3CC[C@@H](C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 7, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 10, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 44
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057527 none O=C([O-])C1=CC=C(NC(=O)NN=C2C[C@@H]3CC[C@@H](C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 7, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 20
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 22, 23, 24, 25, 26, 27])
total number of confs: 49
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057527 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057527
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057527/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057527
Building REAL300000057528
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057528'
/scratch/stefan/7769638/working/building/REAL300000057528 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057528

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057528/0 /scratch/stefan/7769638/working/building/REAL300000057528 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 551)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/551
`/scratch/stefan/7769638/working/3D/551' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2CCOC3)C=C1)

`REAL300000057528.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057528.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057528/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057528 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2CCOC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 32, 32, 49, 49, 42, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 8, 14, 32, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1] 49
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057528 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2CCOC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 24, 24, 24, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 24, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52] 52
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 23, 24, 25, 26, 27, 28, 29, 39])
total number of confs: 141
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057528 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057528
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057528/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057528
Building REAL300000057529
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057529'
/scratch/stefan/7769638/working/building/REAL300000057529 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057529

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057529/0 /scratch/stefan/7769638/working/building/REAL300000057529 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 552)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/552
`/scratch/stefan/7769638/working/3D/552' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=C(C)C=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C)

`REAL300000057529.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057529.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057529/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057529 none COCC1=C(C)C=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 5, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 97, 107, 107, 103, 107, 107, 107, 107, 107, 1, 1, 21, 21, 21, 6, 6, 2, 2, 2, 1, 2, 2, 2, 7, 37, 97, 107, 107, 107, 107, 2, 2, 2] 171
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 25, 26] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 349
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057529 none COCC1=C(C)C=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 5, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [171, 171, 107, 107, 46, 65, 107, 107, 107, 43, 43, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 171, 171, 171, 171, 171, 107, 107, 107, 107, 107, 107, 107, 43, 15, 7, 1, 1, 1, 1, 107, 107, 107] 171
rigid atoms, others: [42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48])
total number of confs: 867
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057529 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057529
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057529/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057529
Building REAL300000057530
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057530'
/scratch/stefan/7769638/working/building/REAL300000057530 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057530

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057530/0 /scratch/stefan/7769638/working/building/REAL300000057530 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 553)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/553
`/scratch/stefan/7769638/working/3D/553' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OC(=O)OC3=C2)C=C1)

`REAL300000057530.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057530.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057530/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057530 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OC(=O)OC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'O.3', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 11, 12, 1, 1, 1, 1, 7, 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, 3, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 12, 12, 12, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 9, 12, 28, 49, 49, 49, 1, 1] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 23, 24, 25, 26] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 94
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057530 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OC(=O)OC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'O.3', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 11, 12, 1, 1, 1, 1, 7, 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, 3, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 21, 20, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 20, 6, 1, 1, 1, 49, 49] 49
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 33, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 133
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057530 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057530
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057530/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057530
Building REAL300000057531
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057531'
/scratch/stefan/7769638/working/building/REAL300000057531 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057531

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057531/0 /scratch/stefan/7769638/working/building/REAL300000057531 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 554)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/554
`/scratch/stefan/7769638/working/3D/554' -> `0.mol2'
Preparing input files

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

`REAL300000057531.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057531.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057531/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057531 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C=C(N)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 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, 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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 7, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 39
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057531 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C=C(N)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 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, 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: [4, 1, 4, 4, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 18, 18, 18, 18, 18, 2, 2, 2, 1, 2, 2, 1, 2, 2, 2] 18
rigid atoms, others: [1, 37, 40, 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, 36, 38, 39, 41, 42, 43])
total number of confs: 65
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057531 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057531
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057531/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057531
Building REAL300000057532
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057532'
/scratch/stefan/7769638/working/building/REAL300000057532 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057532

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057532/0 /scratch/stefan/7769638/working/building/REAL300000057532 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 555)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/555
`/scratch/stefan/7769638/working/3D/555' -> `0.mol2'
Preparing input files

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

`REAL300000057532.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057532.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057532/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057532 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C=C(O)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 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, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 6, 1, 1, 1, 1, 18, 18, 18, 18, 36, 18, 18, 18, 18] 36
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 74
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057532 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C=C(O)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 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: [4, 1, 4, 4, 8, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 18, 18, 18, 18, 18, 2, 2, 2, 1, 2, 1, 2, 2, 2] 36
rigid atoms, others: [1, 37, 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, 36, 38, 40, 41, 42])
total number of confs: 69
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057532 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057532
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057532/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057532
Building REAL300000057533
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057533'
/scratch/stefan/7769638/working/building/REAL300000057533 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057533

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057533/0 /scratch/stefan/7769638/working/building/REAL300000057533 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 556)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/556
`/scratch/stefan/7769638/working/3D/556' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Br)C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057533.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057533.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057533/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057533 none CC1=C(Br)C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 6, 6, 14, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 1, 6, 14, 39, 39, 39, 39, 39] 39
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057533 none CC1=C(Br)C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 30, 30, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 30, 10, 7, 1, 1, 1, 1] 39
rigid atoms, others: [32, 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: 72
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057533 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057533
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057533/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057533
Building REAL300000057534
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057534'
/scratch/stefan/7769638/working/building/REAL300000057534 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057534

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057534/0 /scratch/stefan/7769638/working/building/REAL300000057534 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 557)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/557
`/scratch/stefan/7769638/working/3D/557' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC2=C(C=C1OC)C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CCCC2)

`REAL300000057534.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057534.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057534/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057534 none COC1=CC2=C(C=C1OC)C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 4, 7, 6, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 6, 7, 7, 18, 23, 23, 21, 23, 23, 23, 23, 23, 1, 1, 1, 1, 3, 3, 3, 1, 1, 4, 4, 4, 6, 18, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1] 33
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 25, 26, 27, 28, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50] set([0, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057534 none COC1=CC2=C(C=C1OC)C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 4, 7, 6, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 23, 23, 23, 23, 23, 23, 23, 23, 33, 23, 11, 11, 6, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 23, 23, 23, 23, 33, 33, 33, 23, 23, 33, 33, 33, 11, 6, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23] 33
rigid atoms, others: [39, 40, 41, 42, 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, 36, 37, 38, 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
/scratch/stefan/7769638/working/building/REAL300000057534 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057534
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057534/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057534
Building REAL300000057535
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057535'
/scratch/stefan/7769638/working/building/REAL300000057535 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057535

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057535/0 /scratch/stefan/7769638/working/building/REAL300000057535 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 558)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/558
`/scratch/stefan/7769638/working/3D/558' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCO1)

`REAL300000057535.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057535.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057535/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057535 none CC(C)(C)C1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 3, 2, 2, 2, 3, 3, 3, 1, 1, 1, 9, 21, 21, 21, 21, 21, 1, 1, 1, 1] 21
rigid atoms, others: [1, 34, 35, 4, 5, 6, 33, 8, 42, 7, 44, 45, 43, 21, 22, 23] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 73
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057535 none CC(C)(C)C1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 7, 1, 1, 1, 1, 21, 21, 21, 21] 21
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 46
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057535 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057535
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057535/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057535
Building REAL300000057536
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057536'
/scratch/stefan/7769638/working/building/REAL300000057536 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057536

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057536/0 /scratch/stefan/7769638/working/building/REAL300000057536 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 559)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/559
`/scratch/stefan/7769638/working/3D/559' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC=CC=C2S1)

`REAL300000057536.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057536.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057536/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057536 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 9, 25, 28, 28, 25, 27, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 9, 25, 28, 28, 28, 28, 1, 1, 1, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 100
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057536 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 7, 1, 1, 1, 1, 28, 28, 28, 28] 28
rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43])
total number of confs: 59
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057536 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057536
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057536/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057536
Building REAL300000057537
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057537'
/scratch/stefan/7769638/working/building/REAL300000057537 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057537

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057537/0 /scratch/stefan/7769638/working/building/REAL300000057537 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 560)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/560
`/scratch/stefan/7769638/working/3D/560' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)C=C1)

`REAL300000057537.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057537.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057537/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057537 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'Cl', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 3, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057537 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'Cl', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [129, 120, 129, 113, 129, 129, 107, 38, 37, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 129, 129, 129, 129, 107, 37, 11, 1, 1, 1, 3, 3, 3, 3, 1, 129, 129] 129
rigid atoms, others: [33, 34, 35, 40, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057537 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'Cl', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [129, 129, 129, 129, 129, 129, 125, 60, 60, 60, 18, 18, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 129, 129, 129, 129, 125, 60, 18, 3, 3, 3, 1, 1, 1, 1, 3, 129, 129] 129
rigid atoms, others: [36, 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, 40, 41, 42])
total number of confs: 352
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057537 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057537
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057537/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057537
Building REAL300000057538
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057538'
/scratch/stefan/7769638/working/building/REAL300000057538 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057538

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057538/0 /scratch/stefan/7769638/working/building/REAL300000057538 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 561)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/561
`/scratch/stefan/7769638/working/3D/561' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=NC=CC=C23)C=C1)

`REAL300000057538.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057538.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057538/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057538 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=NC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 15, 15, 15, 38, 38, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 8, 15, 38, 55, 55, 55, 55, 55, 55, 1, 1] 55
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: 102
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057538 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=NC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 31, 31, 31, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 31, 10, 1, 1, 1, 1, 1, 1, 55, 55] 55
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 37, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057538 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057538
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057538/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057538
Building REAL300000057539
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057539'
/scratch/stefan/7769638/working/building/REAL300000057539 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057539

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057539/0 /scratch/stefan/7769638/working/building/REAL300000057539 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 562)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/562
`/scratch/stefan/7769638/working/3D/562' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C([N+](=O)[O-])=N1)

`REAL300000057539.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057539.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057539/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057539 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C([N+](=O)[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 2, 2, 1, 2, 2, 2, 1, 8, 22, 50, 50, 50, 50, 50] 50
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 145
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057539 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C([N+](=O)[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 41, 41, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 15, 7, 1, 1, 1, 1] 50
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057539 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057539
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057539/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057539
Building REAL300000057540
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057540'
/scratch/stefan/7769638/working/building/REAL300000057540 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057540

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057540/0 /scratch/stefan/7769638/working/building/REAL300000057540 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 563)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/563
`/scratch/stefan/7769638/working/3D/563' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C)

`REAL300000057540.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057540.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057540/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057540 none CCCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 29, 7, 1, 1, 1, 1, 1, 1, 6, 6, 18, 19, 19, 65, 88, 88, 72, 88, 88, 88, 88, 88, 1, 1, 1, 51, 51, 51, 50, 50, 29, 29, 1, 1, 6, 18, 65, 88, 88, 88, 88, 1, 2, 2, 2] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 42, 23, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45])
total number of confs: 543
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057540 none CCCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 145, 45, 34, 88, 88, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 88, 88, 88, 201, 201, 201, 201, 201, 199, 198, 88, 88, 34, 16, 7, 1, 1, 1, 1, 88, 88, 88, 88] 201
rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 699
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057540 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057540
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057540/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057540
Building REAL300000057541
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057541'
/scratch/stefan/7769638/working/building/REAL300000057541 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057541

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057541/0 /scratch/stefan/7769638/working/building/REAL300000057541 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 564)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/564
`/scratch/stefan/7769638/working/3D/564' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=NC=CN=C3C=C2)C=C1)

`REAL300000057541.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057541.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057541/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057541 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=NC=CN=C3C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 5, 5, 9, 9, 9, 9, 9, 1, 1] 9
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: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057541 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=NC=CN=C3C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 25, 25, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 25, 7, 1, 1, 1, 1, 1, 44, 44] 44
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 117
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057541 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057541
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057541/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057541
Building REAL300000057542
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057542'
/scratch/stefan/7769638/working/building/REAL300000057542 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057542

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057542/0 /scratch/stefan/7769638/working/building/REAL300000057542 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 565)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/565
`/scratch/stefan/7769638/working/3D/565' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1CN1C=CC=N1)

`REAL300000057542.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057542.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057542/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057542 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1CN1C=CC=N1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 8, 8, 17, 18, 18, 42, 51, 51, 42, 47, 51, 51, 51, 51, 1, 1, 1, 7, 23, 23, 23, 23, 4, 4, 4, 1, 1, 8, 17, 42, 51, 51, 51, 51, 1, 7, 7, 23, 23, 23] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 41, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057542 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1CN1C=CC=N1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [83, 51, 51, 51, 51, 16, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 51, 51, 51, 120, 201, 201, 201, 201, 83, 83, 83, 51, 51, 16, 6, 6, 1, 1, 1, 1, 51, 120, 120, 201, 201, 201] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057542 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1CN1C=CC=N1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 23, 23, 23, 23, 23, 82, 82, 103, 103, 103, 195, 201, 201, 195, 201, 201, 201, 201, 201, 23, 9, 1, 1, 1, 1, 1, 1, 34, 34, 34, 23, 23, 82, 103, 195, 201, 201, 201, 201, 23, 9, 9, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 663
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057542 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057542
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057542/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057542
Building REAL300000057543
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057543'
/scratch/stefan/7769638/working/building/REAL300000057543 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057543

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057543/0 /scratch/stefan/7769638/working/building/REAL300000057543 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 566)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/566
`/scratch/stefan/7769638/working/3D/566' -> `0.mol2'
Preparing input files

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

`REAL300000057543.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057543/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057543 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(O)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7]
1  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 48, 48, 48, 48, 48, 48, 48, 25, 25, 25, 15, 7, 1, 1, 1, 1, 48, 96, 48, 48] 96
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 194
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057543 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(O)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7]
1  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 26, 48, 48, 48, 48, 48, 1, 2, 1, 1] 96
rigid atoms, others: [1, 35, 36, 33, 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, 34])
total number of confs: 137
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057543 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057543
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057543/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057543
Building REAL300000057544
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057544'
/scratch/stefan/7769638/working/building/REAL300000057544 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057544

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057544/0 /scratch/stefan/7769638/working/building/REAL300000057544 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 567)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/567
`/scratch/stefan/7769638/working/3D/567' -> `0.mol2'
Preparing input files

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

`REAL300000057544.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057544.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057544/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057544 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(O)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 48, 48, 48, 48, 48, 48, 48, 27, 27, 27, 15, 7, 1, 1, 1, 1, 48, 48, 48, 96] 96
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 199
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057544 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(O)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 48, 48, 48, 48, 48, 1, 1, 1, 2] 96
rigid atoms, others: [1, 34, 35, 33, 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, 36])
total number of confs: 135
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057544 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057544
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057544/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057544
Building REAL300000057545
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057545'
/scratch/stefan/7769638/working/building/REAL300000057545 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057545

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057545/0 /scratch/stefan/7769638/working/building/REAL300000057545 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 568)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/568
`/scratch/stefan/7769638/working/3D/568' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC=CC(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057545.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057545.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057545/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057545 none CCOC1=CC=CC(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 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, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 44, 45, 45, 123, 143, 143, 123, 123, 143, 143, 143, 143, 37, 37, 37, 37, 37, 1, 1, 1, 12, 44, 123, 143, 143, 143, 143] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 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])
total number of confs: 587
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057545 none CCOC1=CC=CC(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 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, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 190, 143, 139, 143, 59, 143, 143, 143, 46, 46, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 143, 143, 143, 46, 16, 7, 1, 1, 1, 1] 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])
total number of confs: 634
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057545 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057545
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057545/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057545
Building REAL300000057546
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057546'
/scratch/stefan/7769638/working/building/REAL300000057546 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057546

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057546/0 /scratch/stefan/7769638/working/building/REAL300000057546 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 569)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/569
`/scratch/stefan/7769638/working/3D/569' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(Br)C(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057546.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057546.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057546/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057546 none CC1=CC=C(Br)C(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 17, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 12, 12, 39, 39, 39, 84, 84, 84, 84, 84, 84, 84, 84, 84, 2, 2, 2, 1, 1, 12, 39, 84, 84, 84, 84, 84] 84
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 235
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057546 none CC1=CC=C(Br)C(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 17, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 84, 84, 84, 84, 84, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 84, 84, 84, 84, 84, 34, 16, 7, 1, 1, 1, 1] 84
rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 145
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057546 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057546
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057546/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057546
Building REAL300000057547
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057547'
/scratch/stefan/7769638/working/building/REAL300000057547 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057547

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057547/0 /scratch/stefan/7769638/working/building/REAL300000057547 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 570)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/570
`/scratch/stefan/7769638/working/3D/570' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CC=C1[N+](=O)[O-])

`REAL300000057547.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057547.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057547/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057547 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 10, 27, 27, 27, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 27, 58, 58, 58, 58, 58, 1, 1, 1] 58
rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 171
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057547 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 31, 31, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 31, 58, 58, 58, 58, 58, 58, 58, 31, 16, 7, 1, 1, 1, 1, 58, 58, 31] 58
rigid atoms, others: [32, 33, 34, 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, 35, 36, 37])
total number of confs: 166
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057547 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057547
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057547/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057547
Building REAL300000057548
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057548'
/scratch/stefan/7769638/working/building/REAL300000057548 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057548

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057548/0 /scratch/stefan/7769638/working/building/REAL300000057548 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 571)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/571
`/scratch/stefan/7769638/working/3D/571' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C([N+](=O)[O-])C(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057548.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057548/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057548 none CC1=CC=C([N+](=O)[O-])C(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 31, 31, 31, 75, 75, 75, 75, 75, 75, 75, 75, 75, 2, 2, 2, 1, 1, 2, 2, 2, 9, 31, 75, 75, 75, 75, 75] 75
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 29, 30] set([6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 209
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057548 none CC1=CC=C([N+](=O)[O-])C(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 57, 75, 75, 75, 75, 75, 75, 43, 43, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 75, 75, 75, 75, 75, 75, 75, 75, 43, 18, 7, 1, 1, 1, 1] 75
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])
total number of confs: 221
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057548 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057548
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057548/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057548
Building REAL300000057549
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057549'
/scratch/stefan/7769638/working/building/REAL300000057549 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057549

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057549/0 /scratch/stefan/7769638/working/building/REAL300000057549 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 572)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/572
`/scratch/stefan/7769638/working/3D/572' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC(C)(C)C1)

`REAL300000057549.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057549/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057549 none C[C@H]1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC(C)(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 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, 7, 7, 4, 7, 6, 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
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, 7, 7, 7, 27, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 27, 28, 28, 28, 28, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 44, 19, 20, 21, 22, 23, 36, 27, 28, 35] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42])
total number of confs: 87
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057549 none C[C@H]1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC(C)(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 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, 7, 7, 4, 7, 6, 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
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, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 7, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 28
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 61
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057549 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057549
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057549/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057549
Building REAL300000057550
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057550'
/scratch/stefan/7769638/working/building/REAL300000057550 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057550

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057550/0 /scratch/stefan/7769638/working/building/REAL300000057550 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 573)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/573
`/scratch/stefan/7769638/working/3D/573' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(O)=C1)

`REAL300000057550.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057550.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057550/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057550 none CC1=CC=C(C=NNC(=O)NC2=CC=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', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 2, 2, 2, 1, 1, 8, 10, 22, 22, 22, 22, 22, 2, 1] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 36, 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, 35])
total number of confs: 65
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057550 none CC1=CC=C(C=NNC(=O)NC2=CC=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', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 18, 18, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 18, 8, 5, 1, 1, 1, 1, 44, 22] 44
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 90
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057550 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057550
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057550/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057550
Building REAL300000057551
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057551'
/scratch/stefan/7769638/working/building/REAL300000057551 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057551

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057551/0 /scratch/stefan/7769638/working/building/REAL300000057551 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 574)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/574
`/scratch/stefan/7769638/working/3D/574' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)C=C1)

`REAL300000057551.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057551/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057551 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 22, 22, 22, 1, 1, 1, 1, 5, 5, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 22, 22, 1, 1] 48
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 7, 51, 52, 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, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 150
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057551 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 19, 22, 19, 22, 22, 19, 9, 8, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 8, 10, 10, 1, 1, 1, 22, 22, 22, 22, 19, 8, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 1, 1, 22, 22] 47
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 36, 37, 38, 39, 40, 41, 49, 50] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 51, 52])
total number of confs: 116
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057551 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 28, 28, 10, 10, 10, 10, 10, 10, 10, 10, 3, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 47, 47, 47, 47, 47, 28, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 10, 10, 47, 47] 47
rigid atoms, others: [44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51, 52])
total number of confs: 140
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057551 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057551/1 /scratch/stefan/7769638/working/building/REAL300000057551 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 575)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/575
`/scratch/stefan/7769638/working/3D/575' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)C=C1)

`REAL300000057551.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057551/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057551 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 54, 54, 54, 54, 54, 54, 28, 28, 28, 1, 1, 1, 1, 8, 10, 28, 28, 28, 28, 28, 28, 54, 54, 54, 54, 54, 54, 54, 28, 28, 1, 1] 54
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 7, 51, 52, 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, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 175
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057551 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 27, 27, 27, 24, 9, 8, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 5, 7, 7, 1, 1, 1, 27, 27, 27, 27, 24, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 1, 1, 27, 27] 54
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 36, 37, 38, 39, 40, 41, 49, 50] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 51, 52])
total number of confs: 96
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057551 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 54, 54, 54, 54, 54, 24, 7, 7, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 7, 7, 54, 54] 54
rigid atoms, others: [44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51, 52])
total number of confs: 162
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057551 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057551
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057551/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057551/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057551
Building REAL300000057552
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057552'
/scratch/stefan/7769638/working/building/REAL300000057552 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057552

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057552/0 /scratch/stefan/7769638/working/building/REAL300000057552 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 576)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/576
`/scratch/stefan/7769638/working/3D/576' -> `0.mol2'
Preparing input files

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

`REAL300000057552.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057552/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057552 none COC(=O)C1=C(C)NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 45, 53, 53, 45, 45, 53, 53, 53, 53, 1, 9, 9, 9, 2, 2, 2, 1, 7, 22, 45, 53, 53, 53, 53, 1] 66
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 39, 24, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 219
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057552 none COC(=O)C1=C(C)NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 53, 66, 53, 53, 53, 53, 30, 30, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 53, 66, 66, 66, 53, 53, 53, 53, 30, 10, 6, 1, 1, 1, 1, 53] 66
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057552 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057552
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057552/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057552
Building REAL300000057553
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057553'
/scratch/stefan/7769638/working/building/REAL300000057553 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057553

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057553/0 /scratch/stefan/7769638/working/building/REAL300000057553 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 577)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/577
`/scratch/stefan/7769638/working/3D/577' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCO1)

`REAL300000057553.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057553.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057553/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057553 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 9, 25, 25, 25, 25, 25, 1, 1, 1, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 19, 20, 21, 36, 38, 28, 29, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 75
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057553 none CC1(C)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 7, 1, 1, 1, 1, 25, 25, 25, 25] 25
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, 38, 39])
total number of confs: 58
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057553 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057553
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057553/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057553
Building REAL300000057554
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057554'
/scratch/stefan/7769638/working/building/REAL300000057554 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057554

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057554/0 /scratch/stefan/7769638/working/building/REAL300000057554 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 578)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/578
`/scratch/stefan/7769638/working/3D/578' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3(CCCC3)C2)C=C1)

`REAL300000057554.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057554.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057554/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057554 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3(CCCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 8, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 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, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 54
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057554 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3(CCCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 20
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 43, 22, 23, 24, 25, 26, 27])
total number of confs: 49
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057554 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057554
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057554/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057554
Building REAL300000057555
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057555'
/scratch/stefan/7769638/working/building/REAL300000057555 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057555

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057555/0 /scratch/stefan/7769638/working/building/REAL300000057555 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 579)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/579
`/scratch/stefan/7769638/working/3D/579' -> `0.mol2'
Preparing input files

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

`REAL300000057555.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057555.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057555/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057555 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(F)C=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 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, 2, 2, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 16, 16, 16, 12, 7, 1, 1, 1, 1, 25, 25, 25] 25
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37])
total number of confs: 61
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057555 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(F)C=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 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, 2, 2, 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
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, 2, 10, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 10, 25, 25, 25, 25, 25, 1, 1, 1] 25
rigid atoms, others: [1, 35, 36, 37, 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: 75
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057555 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057555
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057555/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057555
Building REAL300000057556
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057556'
/scratch/stefan/7769638/working/building/REAL300000057556 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057556

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057556/0 /scratch/stefan/7769638/working/building/REAL300000057556 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 580)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/580
`/scratch/stefan/7769638/working/3D/580' -> `0.mol2'
Preparing input files

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

`REAL300000057556.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057556.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057556/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057556 none NS(=O)(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 26, 28, 28, 27, 28, 28, 28, 28, 28, 1, 5, 5, 1, 1, 1, 7, 13, 26, 28, 28, 28, 28, 1] 63
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 24, 27, 28, 29, 37] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057556 none NS(=O)(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 28, 63, 63, 28, 22, 28, 28, 20, 20, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 63, 63, 22, 28, 28, 20, 10, 6, 1, 1, 1, 1, 28] 63
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: 228
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057556 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057556
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057556/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057556
Building REAL300000057557
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057557'
/scratch/stefan/7769638/working/building/REAL300000057557 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057557

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057557/0 /scratch/stefan/7769638/working/building/REAL300000057557 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 581)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/581
`/scratch/stefan/7769638/working/3D/581' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN2C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)N=N2)C=C1)

`REAL300000057557.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057557/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057557 none COC1=CC=C(CN2C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 33, 33, 33, 77, 77, 125, 125, 125, 192, 201, 201, 201, 201, 201, 201, 201, 201, 33, 33, 1, 1, 2, 2, 2, 1, 1, 6, 6, 33, 77, 125, 192, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 44, 45, 27, 28] set([0, 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])
total number of confs: 604
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057557 none COC1=CC=C(CN2C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 17, 17, 33, 33, 9, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 37, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 33, 33, 33, 33, 33, 33, 33, 9, 9, 1, 5, 14, 37, 42, 42, 42, 42, 33, 33] 201
rigid atoms, others: [36, 6, 7, 8, 9, 10, 25, 26] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057557 none COC1=CC=C(CN2C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 139, 42, 42, 42, 26, 26, 9, 9, 6, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 42, 42, 201, 201, 201, 201, 201, 201, 201, 139, 139, 42, 26, 9, 6, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [40, 41, 42, 43, 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, 36, 37, 38, 39, 44, 45])
total number of confs: 587
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057557 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057557
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057557/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057557
Building REAL300000057558
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057558'
/scratch/stefan/7769638/working/building/REAL300000057558 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057558

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057558/0 /scratch/stefan/7769638/working/building/REAL300000057558 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 582)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/582
`/scratch/stefan/7769638/working/3D/582' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC3(C2)CCCC3)C=C1)

`REAL300000057558.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057558/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057558 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3(C2)CCCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 7, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1] 26
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 59
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057558 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3(C2)CCCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 27, 27, 26, 9, 8, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 27
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 20, 21, 22, 23, 24, 25, 38])
total number of confs: 74
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057558 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057558
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057558/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057558
Building REAL300000057559
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057559'
/scratch/stefan/7769638/working/building/REAL300000057559 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057559

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057559/0 /scratch/stefan/7769638/working/building/REAL300000057559 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 583)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/583
`/scratch/stefan/7769638/working/3D/583' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=NN2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1)

`REAL300000057559.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057559/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057559 none COC(=O)C1=NN2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 22, 1] 37
rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 25, 26, 42, 30, 31] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41])
total number of confs: 65
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057559 none COC(=O)C1=NN2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 22, 37, 22, 22, 22, 22, 22, 22, 22, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 22, 22, 37, 37, 37, 22, 22, 22, 22, 22, 22, 14, 7, 1, 1, 1, 1, 22] 37
rigid atoms, others: [38, 39, 40, 41, 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, 36, 37, 42])
total number of confs: 110
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057559 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057559
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057559/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057559
Building REAL300000057560
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057560'
/scratch/stefan/7769638/working/building/REAL300000057560 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057560

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057560/0 /scratch/stefan/7769638/working/building/REAL300000057560 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 584)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/584
`/scratch/stefan/7769638/working/3D/584' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1)

`REAL300000057560.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057560.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057560/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057560 none COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 37, 44, 44, 42, 42, 44, 44, 44, 44, 1, 1, 1, 11, 11, 11, 1, 1, 9, 19, 37, 44, 44, 44, 44, 1] 66
rigid atoms, others: [2, 4, 5, 6, 7, 8, 23, 24, 25, 38, 29, 30] set([0, 1, 3, 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: 154
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057560 none COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 44, 66, 44, 44, 44, 28, 28, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 66, 66, 66, 44, 44, 28, 10, 7, 1, 1, 1, 1, 44] 66
rigid atoms, others: [34, 35, 36, 37, 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, 38])
total number of confs: 150
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057560 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057560
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057560/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057560
Building REAL300000057561
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057561'
/scratch/stefan/7769638/working/building/REAL300000057561 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057561

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057561/0 /scratch/stefan/7769638/working/building/REAL300000057561 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 585)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/585
`/scratch/stefan/7769638/working/3D/585' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)C=C1)

`REAL300000057561.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057561.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057561/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057561 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 32, 32, 32, 32, 32, 127, 201, 201, 201, 201, 201, 32, 1, 1, 1, 1, 6, 6, 10, 32, 32, 32, 201, 201, 201, 201, 32, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 309
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057561 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 25, 32, 25, 32, 32, 25, 11, 10, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 25, 1, 32, 32, 32, 32, 25, 10, 6, 1, 1, 1, 25, 25, 25, 25, 1, 32, 32] 201
rigid atoms, others: [33, 34, 35, 40, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057561 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 109, 109, 25, 25, 25, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 201, 201, 201, 201, 201, 125, 109, 25, 25, 25, 1, 1, 1, 1, 25, 201, 201] 201
rigid atoms, others: [36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 579
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057561 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057561
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057561/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057561
Building REAL300000057562
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057562'
/scratch/stefan/7769638/working/building/REAL300000057562 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057562

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057562/0 /scratch/stefan/7769638/working/building/REAL300000057562 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 586)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/586
`/scratch/stefan/7769638/working/3D/586' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CN=C32)C=C1)

`REAL300000057562.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057562/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057562 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CN=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057562 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC=CN=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 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, 4, 3, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 16, 16] 16
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 21, 22, 23, 24, 25, 26])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057562 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057562
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057562/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057562
Building REAL300000057563
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057563'
/scratch/stefan/7769638/working/building/REAL300000057563 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057563

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057563/0 /scratch/stefan/7769638/working/building/REAL300000057563 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 587)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/587
`/scratch/stefan/7769638/working/3D/587' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)C=C1)

`REAL300000057563.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057563/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057563 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 10, 10, 10, 20, 20, 65, 65, 37, 65, 65, 181, 201, 201, 201, 201, 201, 201, 65, 1, 1, 1, 1, 7, 10, 20, 65, 65, 39, 181, 181, 201, 201, 201, 201, 201, 65, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 46, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 685
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057563 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 59, 71, 52, 71, 71, 52, 22, 21, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 15, 15, 14, 15, 15, 1, 71, 71, 71, 71, 52, 21, 8, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 1, 71, 71] 201
rigid atoms, others: [34, 35, 36, 44, 12, 13, 14, 15, 16, 17, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 45, 46])
total number of confs: 337
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057563 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 111, 111, 111, 58, 58, 15, 15, 15, 15, 15, 6, 2, 1, 1, 1, 1, 1, 1, 1, 15, 201, 201, 201, 201, 201, 111, 58, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 15, 201, 201] 201
rigid atoms, others: [39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 632
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057563 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057563
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057563/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057563
Building REAL300000057564
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057564'
/scratch/stefan/7769638/working/building/REAL300000057564 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057564

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057564/0 /scratch/stefan/7769638/working/building/REAL300000057564 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 588)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/588
`/scratch/stefan/7769638/working/3D/588' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2OCC(F)F)C=C1)

`REAL300000057564.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057564/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057564 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2OCC(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 11, 11, 29, 29, 63, 63, 33, 63, 63, 63, 132, 201, 201, 201, 1, 1, 1, 1, 8, 11, 29, 63, 63, 63, 63, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 649
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057564 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2OCC(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 49, 37, 49, 49, 37, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 63, 63, 49, 49, 49, 49, 37, 17, 6, 1, 1, 1, 1, 29, 29, 63, 49, 49] 201
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39])
total number of confs: 441
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057564 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057564
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057564/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057564
Building REAL300000057565
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057565'
/scratch/stefan/7769638/working/building/REAL300000057565 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057565

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057565/0 /scratch/stefan/7769638/working/building/REAL300000057565 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 589)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/589
`/scratch/stefan/7769638/working/3D/589' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1([NH+]2CCCC2)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057565.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057565/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057565 none CC1([NH+]2CCCC2)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 20, 22, 22, 21, 21, 22, 22, 22, 22, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 20, 22, 22, 22, 22, 1, 1, 1, 1] 44
rigid atoms, others: [0, 1, 2, 49, 38, 39, 8, 9, 10, 11, 12, 48, 40, 50, 51, 41, 25, 26] set([3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47])
total number of confs: 81
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057565 none CC1([NH+]2CCCC2)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 43, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 24, 43, 44, 44, 44, 44, 5, 5, 5, 5] 44
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 34, 35, 36, 33, 37, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 119
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057565 none CC1([NH+]2CCCC2)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [22, 22, 22, 44, 44, 44, 44, 44, 22, 22, 22, 8, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 44, 44, 44, 44, 44, 44, 44, 44, 22, 22, 22, 22, 8, 7, 1, 1, 1, 1, 22, 22, 22, 22] 44
rigid atoms, others: [44, 45, 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, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51])
total number of confs: 109
number of broken/clashed sets: 44
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057565 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057565
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057565/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057565
Building REAL300000057566
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057566'
/scratch/stefan/7769638/working/building/REAL300000057566 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057566

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057566/0 /scratch/stefan/7769638/working/building/REAL300000057566 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 590)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/590
`/scratch/stefan/7769638/working/3D/590' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(O)C(F)=C2F)C=C1)

`REAL300000057566.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057566/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057566 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(O)C(F)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7]
1  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 9, 9, 9, 22, 22, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 7, 9, 22, 26, 26, 52, 1, 1] 52
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: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057566 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(O)C(F)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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, 28, 28, 28, 28, 28, 28, 16, 16, 16, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 16, 10, 1, 1, 2, 28, 28] 56
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 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
/scratch/stefan/7769638/working/building/REAL300000057566 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057566/1 /scratch/stefan/7769638/working/building/REAL300000057566 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 591)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/591
`/scratch/stefan/7769638/working/3D/591' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C([O-])C(F)=C2F)C=C1)

`REAL300000057566.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057566/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057566 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C([O-])C(F)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 15, 1, 1, 7, 7, 6, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 8, 8, 8, 22, 22, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 6, 8, 22, 26, 26, 1, 1] 26
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 48
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057566 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C([O-])C(F)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 15, 1, 1, 7, 7, 6, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 34, 35, 34, 35, 35, 34, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 34, 12, 6, 1, 1, 35, 35] 35
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057566 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057566
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057566/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057566/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057566
Building REAL300000057567
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057567'
/scratch/stefan/7769638/working/building/REAL300000057567 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057567

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057567/0 /scratch/stefan/7769638/working/building/REAL300000057567 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 592)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/592
`/scratch/stefan/7769638/working/3D/592' -> `0.mol2'
Preparing input files

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

`REAL300000057567.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057567/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057567 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(O)C=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7]
1  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: [20, 20, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 55, 55, 55, 35, 55, 55, 55, 20, 20, 20, 14, 7, 1, 1, 1, 1, 110, 55, 55, 55] 110
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 307
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057567 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(O)C=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7]
1  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: [9, 1, 9, 9, 23, 23, 23, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 55, 55, 55, 55, 55, 2, 1, 1, 1] 110
rigid atoms, others: [1, 34, 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])
total number of confs: 149
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057567 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057567/1 /scratch/stefan/7769638/working/building/REAL300000057567 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 593)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/593
`/scratch/stefan/7769638/working/3D/593' -> `1.mol2'
Preparing input files

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

`REAL300000057567.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057567/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057567 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C([O-])C=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 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, 2, 2, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 22, 22, 7, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 37, 37, 37, 37, 37, 37, 37, 28, 28, 28, 22, 7, 1, 1, 1, 1, 37, 37, 37] 37
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057567 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C([O-])C=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 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, 2, 2, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 37, 37, 37, 37, 37, 1, 1, 1] 37
rigid atoms, others: [1, 34, 35, 33, 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])
total number of confs: 95
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057567 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057567
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057567/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057567/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057567
Building REAL300000057568
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057568'
/scratch/stefan/7769638/working/building/REAL300000057568 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057568

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057568/0 /scratch/stefan/7769638/working/building/REAL300000057568 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 594)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/594
`/scratch/stefan/7769638/working/3D/594' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CS2)O1)

`REAL300000057568.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057568.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057568/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057568 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CS2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 14, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 13, 13, 47, 47, 47, 110, 120, 120, 110, 112, 120, 120, 120, 120, 1, 1, 1, 13, 13, 13, 13, 1, 2, 2, 2, 13, 47, 110, 120, 120, 120, 120, 13, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 18, 19, 20, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 404
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057568 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CS2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 14, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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: [120, 120, 54, 54, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 201, 201, 201, 201, 120, 120, 120, 120, 54, 16, 7, 1, 1, 1, 1, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 330
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057568 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CS2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 14, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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: [13, 13, 13, 13, 73, 73, 122, 122, 122, 194, 201, 201, 194, 194, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 72, 122, 194, 201, 201, 201, 201, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 577
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057568 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057568
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057568/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057568
Building REAL300000057569
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057569'
/scratch/stefan/7769638/working/building/REAL300000057569 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057569

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057569/0 /scratch/stefan/7769638/working/building/REAL300000057569 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 595)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/595
`/scratch/stefan/7769638/working/3D/595' -> `0.mol2'
Preparing input files

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

`REAL300000057569.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057569.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057569/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057569 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C#N)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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.1', 'N.1', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 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, 2, 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
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 26, 26, 26, 26, 26, 26, 26, 20, 20, 20, 10, 7, 1, 1, 1, 1, 26, 26, 26] 26
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 55
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057569 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C#N)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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.1', 'N.1', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 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, 2, 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
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [9, 1, 9, 9, 20, 20, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 19, 26, 26, 26, 26, 26, 1, 1, 1] 26
rigid atoms, others: [1, 34, 35, 33, 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])
total number of confs: 70
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057569 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057569
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057569/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057569
Building REAL300000057570
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057570'
/scratch/stefan/7769638/working/building/REAL300000057570 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057570

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057570/0 /scratch/stefan/7769638/working/building/REAL300000057570 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 596)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/596
`/scratch/stefan/7769638/working/3D/596' -> `0.mol2'
Preparing input files

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

`REAL300000057570.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057570.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057570/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057570 none COC(=O)C1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 8, 8, 8, 41, 41, 41, 73, 81, 81, 73, 79, 81, 81, 81, 81, 1, 1, 1, 13, 13, 13, 1, 1, 8, 8, 8, 41, 73, 81, 81, 81, 81, 2, 2, 2, 1] 128
rigid atoms, others: [2, 4, 5, 6, 7, 8, 44, 24, 25, 26, 30, 31] set([0, 1, 3, 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])
total number of confs: 297
number of broken/clashed sets: 79
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057570 none COC(=O)C1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [120, 120, 42, 120, 42, 81, 81, 42, 42, 42, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 81, 81, 81, 120, 120, 120, 81, 81, 42, 42, 42, 14, 7, 1, 1, 1, 1, 81, 81, 81, 81] 128
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44])
total number of confs: 448
number of broken/clashed sets: 79
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057570 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057570
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057570/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057570
Building REAL300000057571
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057571'
/scratch/stefan/7769638/working/building/REAL300000057571 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057571

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057571/0 /scratch/stefan/7769638/working/building/REAL300000057571 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 597)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/597
`/scratch/stefan/7769638/working/3D/597' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(CO)=CS2)C=C1)

`REAL300000057571.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057571.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057571/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057571 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(CO)=CS2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 5, 12, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
252  conformations in input
total number of sets (complete confs): 252
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 16, 16, 16, 45, 45, 73, 73, 73, 84, 73, 73, 1, 1, 1, 1, 10, 16, 45, 84, 84, 252, 73, 1, 1] 252
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 451
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057571 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(CO)=CS2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 5, 12, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
261  conformations in input
total number of sets (complete confs): 261
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 75, 76, 76, 72, 29, 29, 29, 7, 7, 1, 1, 1, 1, 1, 8, 1, 1, 76, 76, 76, 76, 72, 28, 7, 8, 8, 24, 1, 76, 76] 261
rigid atoms, others: [12, 13, 14, 15, 16, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 253
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057571 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057571
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057571/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057571
Building REAL300000057572
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057572'
/scratch/stefan/7769638/working/building/REAL300000057572 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057572

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057572/0 /scratch/stefan/7769638/working/building/REAL300000057572 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 598)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/598
`/scratch/stefan/7769638/working/3D/598' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(N2C=CN=C2)=C1)

`REAL300000057572.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057572/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057572 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 80, 80, 80, 80, 80, 139, 139, 139, 139, 80, 34, 34, 34, 15, 7, 1, 1, 1, 1, 80, 80, 80, 139, 139, 139, 80] 139
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 253
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057572 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 39, 39, 39, 75, 80, 80, 78, 78, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 11, 11, 11, 39, 75, 80, 80, 80, 80, 1, 1, 1, 9, 9, 9, 1] 139
rigid atoms, others: [1, 36, 37, 38, 42, 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, 39, 40, 41])
total number of confs: 241
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057572 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [49, 9, 49, 49, 92, 92, 92, 137, 139, 139, 139, 139, 139, 139, 139, 139, 9, 8, 9, 9, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 92, 137, 139, 139, 139, 139, 8, 9, 9, 1, 1, 1, 9] 139
rigid atoms, others: [39, 40, 41, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42])
total number of confs: 377
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057572 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057572
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057572/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057572
Building REAL300000057573
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057573'
/scratch/stefan/7769638/working/building/REAL300000057573 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057573

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057573/0 /scratch/stefan/7769638/working/building/REAL300000057573 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 599)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/599
`/scratch/stefan/7769638/working/3D/599' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3(CCCCC3)C2)C=C1)

`REAL300000057573.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057573.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057573/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057573 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3(CCCCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 16, 16, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 12, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 46, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 50
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057573 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3(CCCCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 22
rigid atoms, others: [10, 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, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 45, 46, 23, 24, 25, 26, 27, 28])
total number of confs: 53
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057573 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057573
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057573/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057573
Building REAL300000057574
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057574'
/scratch/stefan/7769638/working/building/REAL300000057574 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057574

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057574/0 /scratch/stefan/7769638/working/building/REAL300000057574 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 600)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/600
`/scratch/stefan/7769638/working/3D/600' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3(CCOCC3)C2)C=C1)

`REAL300000057574.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057574.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057574/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057574 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3(CCOCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 11, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 44, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 48
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057574 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3(CCOCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 20
rigid atoms, others: [10, 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, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 43, 44, 23, 24, 25, 26, 27, 28])
total number of confs: 47
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057574 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057574
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057574/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057574
Building REAL300000057575
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057575'
/scratch/stefan/7769638/working/building/REAL300000057575 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057575

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057575/0 /scratch/stefan/7769638/working/building/REAL300000057575 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 601)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/601
`/scratch/stefan/7769638/working/3D/601' -> `0.mol2'
Preparing input files

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

`REAL300000057575.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057575.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057575/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057575 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(C#N)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [73, 50, 50, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 110, 110, 110, 110, 110, 110, 110, 73, 73, 73, 73, 73, 16, 7, 1, 1, 1, 1, 110, 110, 110, 110] 129
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])
total number of confs: 307
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057575 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(C#N)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [28, 12, 1, 12, 12, 52, 53, 53, 107, 110, 110, 110, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 28, 28, 52, 107, 110, 110, 110, 110, 1, 1, 1, 1] 129
rigid atoms, others: [2, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 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: 393
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057575 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057575
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057575/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057575
Building REAL300000057576
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057576'
/scratch/stefan/7769638/working/building/REAL300000057576 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057576

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057576/0 /scratch/stefan/7769638/working/building/REAL300000057576 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 602)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/602
`/scratch/stefan/7769638/working/3D/602' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C2N=CC=CN12)

`REAL300000057576.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057576/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057576 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C2N=CC=CN12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 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: [28, 28, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 40, 40, 40, 40, 40, 40, 40, 40, 28, 28, 28, 12, 7, 1, 1, 1, 1, 40, 40, 40, 40] 40
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 81
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057576 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C2N=CC=CN12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 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: [10, 1, 10, 10, 24, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 24, 40, 40, 40, 40, 40, 1, 1, 1, 1] 40
rigid atoms, others: [1, 34, 35, 36, 37, 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])
total number of confs: 113
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057576 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057576
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057576/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057576
Building REAL300000057577
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057577'
/scratch/stefan/7769638/working/building/REAL300000057577 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057577

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057577/0 /scratch/stefan/7769638/working/building/REAL300000057577 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 603)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/603
`/scratch/stefan/7769638/working/3D/603' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)C=C1)

`REAL300000057577.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057577.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057577/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057577 none O=C([O-])C1=CC=C(NC(=O)NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 5, 10, 10, 26, 32, 32, 32, 32, 32, 32, 10, 22, 22, 22, 22, 22, 1, 1, 1, 1, 3, 5, 26, 26, 32, 32, 32, 32, 32, 32, 32, 22, 22, 22, 22, 1, 1] 57
rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 47, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057577 none O=C([O-])C1=CC=C(NC(=O)NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [138, 134, 138, 122, 138, 138, 121, 65, 65, 65, 28, 28, 7, 3, 1, 1, 1, 1, 1, 1, 1, 28, 61, 61, 61, 61, 61, 138, 138, 138, 138, 121, 65, 7, 7, 3, 3, 1, 1, 1, 1, 1, 61, 61, 61, 61, 138, 138] 201
rigid atoms, others: [37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47])
total number of confs: 546
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057577 none O=C([O-])C1=CC=C(NC(=O)NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 68, 72, 61, 72, 72, 60, 28, 28, 28, 7, 7, 1, 7, 44, 55, 61, 61, 55, 61, 61, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 60, 28, 44, 44, 55, 55, 61, 61, 55, 61, 61, 1, 1, 1, 1, 72, 72] 201
rigid atoms, others: [44, 42, 43, 12, 45, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47])
total number of confs: 475
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057577 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057577
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057577/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057577
Building REAL300000057578
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057578'
/scratch/stefan/7769638/working/building/REAL300000057578 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057578

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057578/0 /scratch/stefan/7769638/working/building/REAL300000057578 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 604)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/604
`/scratch/stefan/7769638/working/3D/604' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)S1)

`REAL300000057578.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057578.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057578/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057578 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [30, 30, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 39, 39, 39, 39, 39, 39, 39, 39, 30, 30, 30, 16, 7, 1, 1, 1, 1, 39, 39] 39
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 80
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057578 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [9, 1, 9, 9, 24, 24, 24, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 10, 10, 23, 39, 39, 39, 39, 39, 1, 1] 39
rigid atoms, others: [1, 34, 35, 16, 17, 18, 19, 20, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 122
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057578 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057578
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057578/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057578
Building REAL300000057579
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057579'
/scratch/stefan/7769638/working/building/REAL300000057579 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057579

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057579/0 /scratch/stefan/7769638/working/building/REAL300000057579 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 605)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/605
`/scratch/stefan/7769638/working/3D/605' -> `0.mol2'
Preparing input files

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

`REAL300000057579.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057579.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057579/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057579 none COC(=O)C1=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C([N+](=O)[O-])[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 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: [9, 9, 1, 9, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 71, 76, 76, 75, 76, 76, 76, 76, 76, 1, 1, 2, 2, 1, 9, 9, 9, 1, 7, 7, 7, 26, 71, 76, 76, 76, 76] 106
rigid atoms, others: [2, 4, 5, 6, 7, 23, 24, 27, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 225
number of broken/clashed sets: 68
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057579 none COC(=O)C1=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C([N+](=O)[O-])[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 76, 106, 76, 76, 46, 46, 46, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 106, 106, 106, 76, 46, 46, 46, 16, 7, 1, 1, 1, 1] 106
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 249
number of broken/clashed sets: 68
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057579 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057579
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057579/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057579
Building REAL300000057580
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057580'
/scratch/stefan/7769638/working/building/REAL300000057580 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000057580

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057580/0 /scratch/stefan/7769638/working/building/REAL300000057580 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 606)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/606
`/scratch/stefan/7769638/working/3D/606' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCCN(C2)C3)C=C1)

`REAL300000057580.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057580/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057580 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCCN(C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 8, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1] 22
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 51
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057580 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCCN(C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 22
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, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 41, 40, 21, 22, 23, 24, 25, 26])
total number of confs: 51
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057580 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057580/1 /scratch/stefan/7769638/working/building/REAL300000057580 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 607)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/607
`/scratch/stefan/7769638/working/3D/607' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC[N@@H+](C2)C3)C=C1)

`REAL300000057580.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057580/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057580 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC[N@@H+](C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 13
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 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, 35, 36, 37, 38, 39, 40])
total number of confs: 34
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057580 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC[N@@H+](C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 13
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 41, 22, 23, 24, 25, 26, 27])
total number of confs: 35
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057580 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `2'
/scratch/stefan/7769638/working/building/REAL300000057580/2 /scratch/stefan/7769638/working/building/REAL300000057580 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 2 (index: 608)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/608
`/scratch/stefan/7769638/working/3D/608' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC[N@H+](C2)C3)C=C1)

`REAL300000057580.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000057580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057580/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057580 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC[N@H+](C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 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, 35, 36, 37, 38, 39, 40])
total number of confs: 27
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057580 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC[N@H+](C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 12
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 41, 22, 23, 24, 25, 26, 27])
total number of confs: 35
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057580 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057580
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057580/0.*
2: /scratch/stefan/7769638/working/building/REAL300000057580/2.*
1: /scratch/stefan/7769638/working/building/REAL300000057580/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057580
Building REAL300000057581
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057581'
/scratch/stefan/7769638/working/building/REAL300000057581 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057581

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057581/0 /scratch/stefan/7769638/working/building/REAL300000057581 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 609)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/609
`/scratch/stefan/7769638/working/3D/609' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(C)(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(F)Cl)

`REAL300000057581.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057581/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057581 none CC1C(C)(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(F)Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'F', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 15, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 7, 7, 19, 19, 19, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 7, 18, 40, 40, 40, 40, 40] 40
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057581 none CC1C(C)(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1(F)Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'F', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 15, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 29, 40, 29, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 29, 14, 7, 1, 1, 1, 1] 40
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 103
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057581 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057581
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057581/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057581
Building REAL300000057582
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057582'
/scratch/stefan/7769638/working/building/REAL300000057582 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057582

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057582/0 /scratch/stefan/7769638/working/building/REAL300000057582 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 610)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/610
`/scratch/stefan/7769638/working/3D/610' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CC(C2)[N@H+](CC2=CC=CC=C2)C3)C=C1)

`REAL300000057582.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057582/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057582 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CC(C2)[N@H+](CC2=CC=CC=C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 7, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 51, 52, 28, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 43
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057582 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CC(C2)[N@H+](CC2=CC=CC=C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 16, 18, 16, 18, 18, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 1, 18, 18, 18, 18, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 1, 1, 18, 18] 18
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 51, 52])
total number of confs: 66
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057582 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CC(C2)[N@H+](CC2=CC=CC=C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 3, 18, 18, 18, 18, 17, 8, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 3, 3, 18, 18] 18
rigid atoms, others: [44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51, 52])
total number of confs: 55
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057582 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057582/1 /scratch/stefan/7769638/working/building/REAL300000057582 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 611)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/611
`/scratch/stefan/7769638/working/3D/611' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CC(C2)[N@@H+](CC2=CC=CC=C2)C3)C=C1)

`REAL300000057582.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057582/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057582 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CC(C2)[N@@H+](CC2=CC=CC=C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 62, 62, 62, 62, 62, 62, 28, 1, 1, 1, 1, 8, 13, 28, 28, 28, 28, 28, 28, 28, 28, 62, 62, 62, 62, 62, 62, 62, 28, 28, 1, 1] 62
rigid atoms, others: [1, 3, 4, 5, 6, 7, 51, 52, 28, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 208
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057582 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CC(C2)[N@@H+](CC2=CC=CC=C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 26, 29, 26, 29, 29, 23, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 5, 7, 7, 1, 29, 29, 29, 29, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 1, 1, 29, 29] 63
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 51, 52])
total number of confs: 116
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057582 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CC(C2)[N@@H+](CC2=CC=CC=C2)C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 59, 28, 28, 28, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 63, 63, 63, 63, 59, 28, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 7, 7, 63, 63] 63
rigid atoms, others: [44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51, 52])
total number of confs: 178
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057582 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057582
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057582/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057582/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057582
Building REAL300000057583
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057583'
/scratch/stefan/7769638/working/building/REAL300000057583 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057583

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057583/0 /scratch/stefan/7769638/working/building/REAL300000057583 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 612)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/612
`/scratch/stefan/7769638/working/3D/612' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)OC)C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1)

`REAL300000057583.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057583.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057583/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057583 none CCC1=C(C(=O)OC)C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 12, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 12, 12, 12, 1, 1, 1, 6, 6, 26, 27, 27, 66, 87, 87, 76, 77, 87, 87, 87, 87, 1, 6, 6, 6, 6, 6, 13, 13, 13, 1, 6, 26, 66, 87, 87, 87, 87, 1] 182
rigid atoms, others: [1, 2, 3, 4, 8, 9, 10, 34, 25, 42] set([0, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 344
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057583 none CCC1=C(C(=O)OC)C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 12, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [143, 87, 87, 87, 87, 150, 150, 150, 87, 42, 42, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 87, 143, 143, 143, 143, 143, 150, 150, 150, 87, 42, 12, 7, 1, 1, 1, 1, 87] 182
rigid atoms, others: [38, 39, 40, 41, 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, 36, 37, 42])
total number of confs: 665
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057583 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057583
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057583/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057583
Building REAL300000057584
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057584'
/scratch/stefan/7769638/working/building/REAL300000057584 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057584

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057584/0 /scratch/stefan/7769638/working/building/REAL300000057584 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 613)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/613
`/scratch/stefan/7769638/working/3D/613' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CN(C(=O)OC(C)(C)C)C1)

`REAL300000057584.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057584.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057584/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057584 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CN(C(=O)OC(C)(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 20, 20, 8, 8, 7, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 69, 69, 69, 96, 96, 161, 164, 164, 164, 69, 34, 34, 34, 34, 34, 8, 7, 1, 1, 1, 1, 69, 69, 69, 164, 164, 164, 164, 164, 164, 164, 164, 164, 69, 69] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 484
number of broken/clashed sets: 157
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057584 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CN(C(=O)OC(C)(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 8, 8, 26, 26, 26, 54, 69, 69, 54, 62, 69, 69, 69, 69, 1, 1, 1, 1, 2, 2, 8, 10, 10, 10, 1, 15, 15, 15, 15, 15, 26, 54, 69, 69, 69, 69, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 201
rigid atoms, others: [51, 2, 39, 40, 41, 17, 18, 19, 20, 52, 27] set([0, 1, 3, 4, 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, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 346
number of broken/clashed sets: 157
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057584 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057584
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057584/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057584
Building REAL300000057585
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057585'
/scratch/stefan/7769638/working/building/REAL300000057585 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057585

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057585/0 /scratch/stefan/7769638/working/building/REAL300000057585 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 614)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/614
`/scratch/stefan/7769638/working/3D/614' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Cl)C=N2)C=C1)

`REAL300000057585.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057585.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057585/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057585 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Cl)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 7, 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, 3, 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, 6, 8, 8, 8, 18, 18, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 6, 8, 18, 20, 20, 20, 1, 1] 20
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 44
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057585 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Cl)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 13, 12, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 12, 6, 1, 1, 1, 22, 22] 22
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, 31])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057585 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057585
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057585/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057585
Building REAL300000057586
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057586'
/scratch/stefan/7769638/working/building/REAL300000057586 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057586

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057586/0 /scratch/stefan/7769638/working/building/REAL300000057586 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 615)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/615
`/scratch/stefan/7769638/working/3D/615' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC1COCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057586.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057586.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057586/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057586 none CC(C)CC1COCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 23] 23
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 36] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42])
total number of confs: 73
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057586 none CC(C)CC1COCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 7, 1, 1, 1, 1] 23
rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 55
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057586 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057586
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057586/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057586
Building REAL300000057587
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057587'
/scratch/stefan/7769638/working/building/REAL300000057587 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057587

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057587/0 /scratch/stefan/7769638/working/building/REAL300000057587 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 616)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/616
`/scratch/stefan/7769638/working/3D/616' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057587.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057587.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057587/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057587 none COC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 27, 33, 33, 27, 27, 33, 33, 33, 33, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 27, 33, 33, 33, 33, 1, 1, 1, 1] 33
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 39, 40, 21, 22, 26, 27, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 33, 34, 35, 36, 37, 38])
total number of confs: 122
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057587 none COC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 16, 7, 1, 1, 1, 1, 33, 33, 33, 33] 33
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 71
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057587 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057587
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057587/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057587
Building REAL300000057588
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057588'
/scratch/stefan/7769638/working/building/REAL300000057588 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057588

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057588/0 /scratch/stefan/7769638/working/building/REAL300000057588 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 617)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/617
`/scratch/stefan/7769638/working/3D/617' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC=CC2=CC=CC(F)=C2)C=C1)

`REAL300000057588.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057588.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057588/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057588 none O=C([O-])C1=CC=C(NC(=O)NN=CC=CC2=CC=CC(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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, 5, 5, 5, 5, 7, 7, 8, 8, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 5, 5, 7, 8, 8, 13, 13, 13, 13, 1, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 36] set([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: 29
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057588 none O=C([O-])C1=CC=C(NC(=O)NN=CC=CC2=CC=CC(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [100, 100, 100, 100, 100, 100, 100, 55, 55, 55, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 55, 26, 6, 6, 1, 1, 1, 1, 100, 100] 100
rigid atoms, others: [32, 33, 34, 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, 35, 36])
total number of confs: 291
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057588 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057588
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057588/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057588
Building REAL300000057589
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057589'
/scratch/stefan/7769638/working/building/REAL300000057589 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057589

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057589/0 /scratch/stefan/7769638/working/building/REAL300000057589 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 618)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/618
`/scratch/stefan/7769638/working/3D/618' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC[C@@H]3[C@H]4OCC[C@H]4[C@H]23)C=C1)

`REAL300000057589.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057589/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057589 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[C@@H]3[C@H]4OCC[C@H]4[C@H]23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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, 11, 8, 8, 1, 5, 5, 5, 7, 5, 7, 12, 5, 5, 5, 7, 5, 7, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 8, 14, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057589 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC[C@@H]3[C@H]4OCC[C@H]4[C@H]23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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, 11, 8, 8, 1, 5, 5, 5, 7, 5, 7, 12, 5, 5, 5, 7, 5, 7, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 18
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 40, 41, 26, 27, 28, 29, 30, 31])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057589 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057589
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057589/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057589
Building REAL300000057590
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057590'
/scratch/stefan/7769638/working/building/REAL300000057590 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057590

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057590/0 /scratch/stefan/7769638/working/building/REAL300000057590 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 619)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/619
`/scratch/stefan/7769638/working/3D/619' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CN=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057590.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057590.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057590/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057590 none COC(=O)C1=CN=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 59, 59, 59, 116, 134, 134, 128, 134, 134, 134, 134, 134, 1, 13, 13, 13, 1, 1, 13, 13, 13, 59, 116, 134, 134, 134, 134, 1] 165
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 40, 25, 29, 30] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 419
number of broken/clashed sets: 123
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057590 none COC(=O)C1=CN=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [165, 165, 134, 165, 134, 134, 134, 134, 36, 36, 36, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 134, 165, 165, 165, 134, 134, 36, 36, 36, 12, 7, 1, 1, 1, 1, 134] 165
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])
total number of confs: 292
number of broken/clashed sets: 123
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057590 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057590
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057590/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057590
Building REAL300000057591
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057591'
/scratch/stefan/7769638/working/building/REAL300000057591 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057591

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057591/0 /scratch/stefan/7769638/working/building/REAL300000057591 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 620)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/620
`/scratch/stefan/7769638/working/3D/620' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC(Br)=C2)C=C1)

`REAL300000057591.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057591/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057591 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC(Br)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.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, 11, 8, 8, 1, 1, 1, 8, 1, 17, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 30, 30, 49, 49, 49, 49, 49, 1, 1, 1, 1, 10, 13, 30, 49, 49, 49, 1, 1] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057591 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC(Br)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.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, 11, 8, 8, 1, 1, 1, 8, 1, 17, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 25, 25, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 25, 7, 1, 1, 1, 49, 49] 49
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057591 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057591
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057591/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057591
Building REAL300000057592
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057592'
/scratch/stefan/7769638/working/building/REAL300000057592 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057592

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057592/0 /scratch/stefan/7769638/working/building/REAL300000057592 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 621)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/621
`/scratch/stefan/7769638/working/3D/621' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NN1)

`REAL300000057592.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057592.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057592/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057592 none CC1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 9, 9, 21, 22, 22, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 2, 2, 2, 2, 2, 2, 9, 21, 52, 52, 52, 52, 52, 1] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 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])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057592 none CC1=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 32, 32, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 32, 12, 7, 1, 1, 1, 1, 52] 52
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057592 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057592
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057592/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057592
Building REAL300000057593
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057593'
/scratch/stefan/7769638/working/building/REAL300000057593 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057593

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057593/0 /scratch/stefan/7769638/working/building/REAL300000057593 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 622)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/622
`/scratch/stefan/7769638/working/3D/622' -> `0.mol2'
Preparing input files

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

`REAL300000057593.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057593.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057593/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057593 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 2, 2, 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
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 21, 21, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 58, 58, 58, 58, 58, 58, 58, 58, 35, 35, 35, 21, 7, 1, 1, 1, 1, 58, 58, 58] 58
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 115
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057593 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 2, 2, 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
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 19, 19, 19, 56, 58, 58, 56, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 19, 56, 58, 58, 58, 58, 1, 1, 1] 58
rigid atoms, others: [1, 34, 35, 36, 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])
total number of confs: 167
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057593 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057593
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057593/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057593
Building REAL300000057594
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057594'
/scratch/stefan/7769638/working/building/REAL300000057594 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057594

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057594/0 /scratch/stefan/7769638/working/building/REAL300000057594 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 623)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/623
`/scratch/stefan/7769638/working/3D/623' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1OC)

`REAL300000057594.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057594.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057594/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057594 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 12, 5, 7, 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, 7, 4, 7, 6, 4, 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]
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: [3, 1, 1, 1, 1, 1, 1, 11, 11, 28, 29, 29, 77, 84, 84, 77, 78, 84, 84, 84, 84, 1, 1, 1, 1, 6, 4, 4, 4, 1, 1, 11, 28, 77, 84, 84, 84, 84, 7, 7, 7] 112
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 276
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057594 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(F)=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 12, 5, 7, 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, 7, 4, 7, 6, 4, 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]
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, 84, 84, 84, 84, 47, 47, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 112, 112, 112, 112, 84, 84, 47, 18, 7, 1, 1, 1, 1, 112, 112, 112] 112
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40])
total number of confs: 249
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057594 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057594
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057594/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057594
Building REAL300000057595
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057595'
/scratch/stefan/7769638/working/building/REAL300000057595 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057595

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057595/0 /scratch/stefan/7769638/working/building/REAL300000057595 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 624)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/624
`/scratch/stefan/7769638/working/3D/624' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057595.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057595.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057595/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057595 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 5, 2, 5, 5, 5, 1, 1, 1, 1, 12, 12, 44, 44, 44, 87, 93, 93, 92, 93, 93, 93, 93, 93, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 2, 2, 2, 12, 43, 87, 93, 93, 93, 93] 141
rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 277
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057595 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 35, 35, 87, 87, 87, 137, 141, 141, 141, 141, 141, 141, 141, 141, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 35, 87, 137, 141, 141, 141, 141] 141
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 382
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057595 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 93, 93, 141, 141, 141, 141, 141, 141, 93, 93, 50, 50, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 93, 93, 93, 141, 141, 141, 141, 141, 141, 141, 93, 93, 93, 50, 18, 7, 1, 1, 1, 1] 141
rigid atoms, others: [45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 250
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057595 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057595
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057595/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057595
Building REAL300000057596
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057596'
/scratch/stefan/7769638/working/building/REAL300000057596 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057596

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057596/0 /scratch/stefan/7769638/working/building/REAL300000057596 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 625)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/625
`/scratch/stefan/7769638/working/3D/625' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1SC(F)(F)F)

`REAL300000057596.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057596.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057596/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057596 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1SC(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'S.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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 40, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 120, 120, 120, 120, 120, 120, 201, 201, 201, 201, 40, 40, 40, 18, 7, 1, 1, 1, 1, 120, 120, 120, 120] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 335
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057596 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1SC(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'S.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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 29, 29, 29, 93, 120, 120, 102, 106, 120, 120, 120, 120, 1, 1, 1, 1, 1, 1, 1, 10, 20, 20, 20, 7, 7, 7, 29, 93, 120, 120, 120, 120, 1, 1, 1, 1] 201
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: 462
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057596 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057596
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057596/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057596
Building REAL300000057597
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057597'
/scratch/stefan/7769638/working/building/REAL300000057597 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057597

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057597/0 /scratch/stefan/7769638/working/building/REAL300000057597 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 626)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/626
`/scratch/stefan/7769638/working/3D/626' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CSC2=CC=CC=C12)

`REAL300000057597.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057597.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057597/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057597 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CSC2=CC=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 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: [32, 32, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 67, 67, 67, 67, 67, 67, 67, 67, 32, 32, 32, 16, 7, 1, 1, 1, 1, 67, 67, 67, 67, 67] 67
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 124
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057597 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CSC2=CC=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 37, 37, 37, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1] 67
rigid atoms, others: [1, 34, 35, 36, 37, 38, 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])
total number of confs: 163
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057597 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057597
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057597/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057597
Building REAL300000057598
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057598'
/scratch/stefan/7769638/working/building/REAL300000057598 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057598

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057598/0 /scratch/stefan/7769638/working/building/REAL300000057598 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 627)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/627
`/scratch/stefan/7769638/working/3D/627' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1)

`REAL300000057598.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057598.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057598/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057598 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
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, 8, 12, 12, 12, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 8, 12, 24, 32, 32, 32, 32, 32, 1, 1] 32
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 25, 26, 27, 28, 37] 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])
total number of confs: 68
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057598 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
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, 18, 18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 18, 8, 1, 1, 1, 1, 1, 53, 53] 53
rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 37, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 139
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057598 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057598
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057598/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057598
Building REAL300000057599
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057599'
/scratch/stefan/7769638/working/building/REAL300000057599 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057599

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057599/0 /scratch/stefan/7769638/working/building/REAL300000057599 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 628)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/628
`/scratch/stefan/7769638/working/3D/628' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])N=C2)C=C1)

`REAL300000057599.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057599.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057599/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057599 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 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, 2, 2, 3, 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, 8, 8, 8, 8, 22, 22, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 8, 8, 22, 43, 43, 43, 1, 1] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 78
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057599 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 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, 2, 2, 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, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 15, 7, 1, 1, 1, 51, 51] 51
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, 33, 32, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 135
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057599 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057599
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057599/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057599
Building REAL300000057600
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057600'
/scratch/stefan/7769638/working/building/REAL300000057600 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057600

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057600/0 /scratch/stefan/7769638/working/building/REAL300000057600 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 629)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/629
`/scratch/stefan/7769638/working/3D/629' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1)

`REAL300000057600.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057600.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057600/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057600 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 26, 26, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 8, 13, 26, 55, 55, 110, 55, 1, 1] 110
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: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057600 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 2, 2, 7, 4, 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, 44, 46, 44, 46, 46, 44, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 46, 46, 46, 46, 44, 26, 7, 1, 1, 2, 1, 46, 46] 92
rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 34, 35])
total number of confs: 145
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057600 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057600
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057600/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057600
Building REAL300000057601
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057601'
/scratch/stefan/7769638/working/building/REAL300000057601 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057601

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057601/0 /scratch/stefan/7769638/working/building/REAL300000057601 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 630)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/630
`/scratch/stefan/7769638/working/3D/630' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C)

`REAL300000057601.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057601.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057601/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057601 none COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [11, 11, 1, 11, 1, 1, 1, 1, 1, 11, 11, 37, 38, 38, 83, 96, 96, 83, 83, 96, 96, 96, 96, 1, 1, 1, 11, 11, 11, 1, 1, 11, 37, 83, 96, 96, 96, 96, 1, 2, 2, 2] 165
rigid atoms, others: [2, 4, 5, 6, 7, 8, 23, 24, 25, 38, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41])
total number of confs: 354
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057601 none COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 72, 165, 66, 96, 96, 40, 40, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 96, 96, 96, 165, 165, 165, 96, 96, 40, 16, 7, 1, 1, 1, 1, 96, 96, 96, 96] 165
rigid atoms, others: [34, 35, 36, 37, 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, 38, 39, 40, 41])
total number of confs: 529
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057601 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057601
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057601/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057601
Building REAL300000057602
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057602'
/scratch/stefan/7769638/working/building/REAL300000057602 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057602

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057602/0 /scratch/stefan/7769638/working/building/REAL300000057602 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 631)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/631
`/scratch/stefan/7769638/working/3D/631' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C(=O)[O-])

`REAL300000057602.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057602.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057602/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057602 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 27, 29, 29, 28, 29, 29, 29, 29, 29, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 15, 27, 29, 29, 29, 29, 1] 29
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 28, 29, 37] 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])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057602 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 6, 6, 1, 1, 1, 1, 29] 29
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057602 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057602
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057602/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057602
Building REAL300000057603
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057603'
/scratch/stefan/7769638/working/building/REAL300000057603 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057603

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057603/0 /scratch/stefan/7769638/working/building/REAL300000057603 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 632)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/632
`/scratch/stefan/7769638/working/3D/632' -> `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)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057603.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057603/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057603 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 47, 53, 53, 49, 53, 53, 53, 53, 53, 1, 10, 24, 47, 53, 53, 53, 53, 1] 53
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 23, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057603 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 28, 28, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 53, 28, 12, 7, 1, 1, 1, 1, 53] 53
rigid atoms, others: [13, 14, 15, 16, 17, 18, 21, 22, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 31])
total number of confs: 96
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057603 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057603
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057603/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057603
Building REAL300000057604
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057604'
/scratch/stefan/7769638/working/building/REAL300000057604 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057604

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057604/0 /scratch/stefan/7769638/working/building/REAL300000057604 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 633)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/633
`/scratch/stefan/7769638/working/3D/633' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CN(C)N=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057604.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057604/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057604 none COC1=CN(C)N=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 8, 5, 8, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 47, 48, 48, 88, 93, 93, 89, 92, 93, 93, 93, 93, 4, 4, 4, 1, 2, 2, 2, 13, 13, 13, 47, 88, 93, 93, 93, 93] 93
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27] set([0, 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])
total number of confs: 279
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057604 none COC1=CN(C)N=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 8, 5, 8, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 93, 93, 93, 93, 33, 33, 33, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 93, 93, 93, 93, 93, 93, 93, 33, 33, 33, 10, 7, 1, 1, 1, 1] 93
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 145
number of broken/clashed sets: 61
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057604 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057604
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057604/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057604
Building REAL300000057605
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057605'
/scratch/stefan/7769638/working/building/REAL300000057605 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057605

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057605/0 /scratch/stefan/7769638/working/building/REAL300000057605 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 634)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/634
`/scratch/stefan/7769638/working/3D/634' -> `0.mol2'
Preparing input files

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

`REAL300000057605.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057605.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057605/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057605 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 5, 15, 15, 15, 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, 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
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 74, 74, 74, 74, 74, 74, 74, 74, 36, 36, 36, 16, 7, 1, 1, 1, 1, 74, 74] 74
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 133
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057605 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 5, 15, 15, 15, 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, 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
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 33, 34, 34, 74, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 12, 12, 33, 74, 74, 74, 74, 74, 1, 1] 74
rigid atoms, others: [1, 34, 35, 16, 17, 18, 19, 20, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 221
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057605 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057605
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057605/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057605
Building REAL300000057606
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057606'
/scratch/stefan/7769638/working/building/REAL300000057606 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057606

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057606/0 /scratch/stefan/7769638/working/building/REAL300000057606 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 635)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/635
`/scratch/stefan/7769638/working/3D/635' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCSC1=CC=CC=C1CC(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057606.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057606.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057606/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057606 none CCSC1=CC=CC=C1CC(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 69, 69, 69, 139, 144, 144, 139, 139, 144, 144, 144, 144, 19, 19, 19, 19, 19, 1, 1, 1, 1, 6, 6, 27, 27, 27, 69, 139, 144, 144, 144, 144] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 557
number of broken/clashed sets: 192
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057606 none CCSC1=CC=CC=C1CC(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 199, 144, 144, 144, 133, 144, 144, 81, 13, 13, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 201, 201, 201, 144, 144, 144, 144, 81, 81, 13, 13, 13, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 539
number of broken/clashed sets: 192
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057606 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057606
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057606/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057606
Building REAL300000057607
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057607'
/scratch/stefan/7769638/working/building/REAL300000057607 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057607

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057607/0 /scratch/stefan/7769638/working/building/REAL300000057607 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 636)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/636
`/scratch/stefan/7769638/working/3D/636' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CN2C(C)(C1)C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CS2(=O)=O)

`REAL300000057607.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057607.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057607/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
Warning: OE3DToAtomStereo is unable to perceive atom stereo from a flat geometry on atom 4 of molecule 'REAL300000057607'
Warning: REAL300000057607 failed due to unspecified stereochemistry with strict stereo enabled
Warning: OE3DToAtomStereo is unable to perceive atom stereo from a flat geometry on atom 4 of molecule 'REAL300000057607'
Warning: REAL300000057607 failed due to unspecified stereochemistry with strict stereo enabled
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
Conformer generation failed
Skipping REAL300000057607 0
/scratch/stefan/7769638/working/building/REAL300000057607 /scratch/stefan/7769638/working /scratch/stefan/7769638
`0' -> `0.failed'

Finished preparing REAL300000057607
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Found failed protomers
Marking REAL300000057607 as failed
mkdir: created directory `/scratch/stefan/7769638/failed'
`/scratch/stefan/7769638/working/building/REAL300000057607' -> `/scratch/stefan/7769638/failed/REAL300000057607'
Building REAL300000057608
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057608'
/scratch/stefan/7769638/working/building/REAL300000057608 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057608

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057608/0 /scratch/stefan/7769638/working/building/REAL300000057608 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 637)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/637
`/scratch/stefan/7769638/working/3D/637' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C#N)=CC(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057608.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057608.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057608/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057608 none CC1=CC(C#N)=CC(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 8, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 35, 35, 2, 2, 2, 1, 1, 2, 2, 2, 7, 15, 35, 35, 35, 35, 35] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057608 none CC1=CC(C#N)=CC(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 8, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 35, 35, 35, 24, 24, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 24, 12, 7, 1, 1, 1, 1] 35
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])
total number of confs: 74
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057608 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057608
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057608/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057608
Building REAL300000057609
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057609'
/scratch/stefan/7769638/working/building/REAL300000057609 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057609

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057609/0 /scratch/stefan/7769638/working/building/REAL300000057609 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 638)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/638
`/scratch/stefan/7769638/working/3D/638' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=C1)CC(C)CC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057609.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057609.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057609/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057609 none COC1=CC=C2C(=C1)CC(C)CC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 46, 46, 36, 41, 46, 46, 46, 46, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 35, 46, 46, 46, 46] 46
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31, 32, 33, 34, 35, 39, 40] set([0, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 41, 42, 43, 44, 45, 46])
total number of confs: 172
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057609 none COC1=CC=C2C(=C1)CC(C)CC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 46, 46, 46, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 14, 7, 1, 1, 1, 1] 46
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: 80
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057609 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057609
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057609/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057609
Building REAL300000057610
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057610'
/scratch/stefan/7769638/working/building/REAL300000057610 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057610

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057610/0 /scratch/stefan/7769638/working/building/REAL300000057610 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 639)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/639
`/scratch/stefan/7769638/working/3D/639' -> `0.mol2'
Preparing input files

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

`REAL300000057610.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057610.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057610/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057610 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 55, 55, 28, 28, 55, 55, 55, 55, 55, 28, 28, 28, 16, 7, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55] 55
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 248
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057610 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 29, 29, 29, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 55, 55, 55, 55, 55, 1, 1, 1, 2, 2, 2] 55
rigid atoms, others: [1, 35, 36, 37, 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, 38, 39, 40])
total number of confs: 153
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057610 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057610
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057610/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057610
Building REAL300000057611
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057611'
/scratch/stefan/7769638/working/building/REAL300000057611 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057611

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057611/0 /scratch/stefan/7769638/working/building/REAL300000057611 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 640)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/640
`/scratch/stefan/7769638/working/3D/640' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057611.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057611.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057611/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057611 none CCOC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 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]
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: [13, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 34, 42, 42, 34, 37, 42, 42, 42, 42, 1, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 9, 34, 42, 42, 42, 42, 1, 1] 53
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 42, 34, 22, 41, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40])
total number of confs: 178
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057611 none CCOC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 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]
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, 42, 42, 42, 42, 42, 42, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 42, 53, 53, 53, 53, 53, 42, 42, 42, 42, 42, 42, 42, 16, 7, 1, 1, 1, 1, 42, 42] 53
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 99
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057611 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057611
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057611/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057611
Building REAL300000057612
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057612'
/scratch/stefan/7769638/working/building/REAL300000057612 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057612

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057612/0 /scratch/stefan/7769638/working/building/REAL300000057612 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 641)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/641
`/scratch/stefan/7769638/working/3D/641' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CS1)

`REAL300000057612.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057612.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057612/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057612 none COC(=O)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 4, 4, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 9, 9, 9, 4, 6, 12, 12, 12, 12, 12, 1, 1] 21
rigid atoms, others: [2, 35, 4, 5, 6, 34, 21, 22, 23] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057612 none COC(=O)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 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]
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, 12, 21, 12, 6, 6, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 12, 12, 21, 21, 21, 6, 4, 4, 1, 1, 1, 1, 12, 12] 21
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 58
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057612 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057612
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057612/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057612
Building REAL300000057613
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057613'
/scratch/stefan/7769638/working/building/REAL300000057613 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057613

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057613/0 /scratch/stefan/7769638/working/building/REAL300000057613 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 642)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/642
`/scratch/stefan/7769638/working/3D/642' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3=CC=C(F)C=C3F)C2)C=C1)

`REAL300000057613.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057613.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057613/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057613 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3=CC=C(F)C=C3F)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', '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, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 34, 34, 34, 34, 65, 65, 45, 65, 65, 65, 65, 34, 1, 1, 1, 1, 10, 13, 34, 34, 34, 65, 65, 65, 34, 34, 1, 1] 65
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 39, 24, 25, 26, 27] set([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: 177
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057613 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3=CC=C(F)C=C3F)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', '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, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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: [34, 33, 34, 33, 34, 34, 30, 10, 9, 10, 1, 1, 1, 1, 1, 1, 9, 9, 1, 7, 9, 9, 9, 1, 34, 34, 34, 34, 30, 9, 1, 1, 1, 9, 9, 9, 1, 1, 34, 34] 66
rigid atoms, others: [32, 36, 37, 10, 11, 12, 13, 14, 15, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 38, 39])
total number of confs: 119
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057613 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3=CC=C(F)C=C3F)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', '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, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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: [66, 66, 66, 66, 66, 66, 63, 33, 33, 33, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 66, 66, 66, 66, 63, 33, 9, 9, 9, 1, 1, 1, 9, 9, 66, 66] 66
rigid atoms, others: [33, 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, 36, 37, 38, 39])
total number of confs: 175
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057613 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057613
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057613/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057613
Building REAL300000057614
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057614'
/scratch/stefan/7769638/working/building/REAL300000057614 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057614

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057614/0 /scratch/stefan/7769638/working/building/REAL300000057614 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 643)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/643
`/scratch/stefan/7769638/working/3D/643' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1COC2=CC=CC=C2C1)

`REAL300000057614.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057614.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057614/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057614 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [26, 26, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 43, 43, 43, 43, 43, 43, 43, 43, 43, 26, 26, 26, 13, 7, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 43
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 120
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057614 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 11, 11, 30, 30, 30, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 30, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1] 43
rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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])
total number of confs: 113
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057614 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057614
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057614/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057614
Building REAL300000057615
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057615'
/scratch/stefan/7769638/working/building/REAL300000057615 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057615

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057615/0 /scratch/stefan/7769638/working/building/REAL300000057615 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 644)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/644
`/scratch/stefan/7769638/working/3D/644' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3CCOCC3)C2)C=C1)

`REAL300000057615.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057615.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057615/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057615 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3CCOCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 36, 36, 36, 36, 36, 36, 49, 49, 49, 49, 49, 36, 1, 1, 1, 1, 10, 13, 36, 36, 36, 36, 36, 36, 36, 49, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36, 1, 1] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 48, 49, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 108
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057615 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3CCOCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [36, 34, 36, 34, 36, 36, 31, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 36, 36, 36, 36, 31, 9, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 36, 36] 49
rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 46, 23, 47, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49])
total number of confs: 114
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057615 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC(C3CCOCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 25, 25, 25, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 49, 49, 49, 49, 49, 25, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 49, 49] 49
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49])
total number of confs: 133
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057615 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057615
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057615/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057615
Building REAL300000057616
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057616'
/scratch/stefan/7769638/working/building/REAL300000057616 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057616

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057616/0 /scratch/stefan/7769638/working/building/REAL300000057616 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 645)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/645
`/scratch/stefan/7769638/working/3D/645' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CCF)N=C2)C=C1)

`REAL300000057616.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057616.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057616/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057616 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CCF)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 15, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 11, 20, 20, 20, 60, 60, 121, 121, 121, 201, 201, 121, 121, 1, 1, 1, 1, 11, 20, 60, 121, 201, 201, 201, 201, 121, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 605
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057616 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CCF)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 15, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 121, 102, 121, 121, 91, 35, 35, 35, 8, 8, 1, 1, 1, 1, 1, 9, 21, 1, 1, 121, 121, 121, 121, 91, 35, 8, 1, 9, 9, 21, 21, 1, 121, 121] 201
rigid atoms, others: [33, 12, 13, 14, 15, 16, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 34, 35])
total number of confs: 481
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057616 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057616
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057616/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057616
Building REAL300000057617
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057617'
/scratch/stefan/7769638/working/building/REAL300000057617 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057617

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057617/0 /scratch/stefan/7769638/working/building/REAL300000057617 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 646)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/646
`/scratch/stefan/7769638/working/3D/646' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=COC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057617.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057617.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057617/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057617 none CC(C)(C)C1=COC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 63, 67, 67, 65, 67, 67, 67, 67, 67, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 7, 27, 63, 67, 67, 67, 67] 71
rigid atoms, others: [1, 4, 5, 6, 33, 8, 7, 23] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 200
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057617 none CC(C)(C)C1=COC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 67, 71, 71, 67, 67, 67, 43, 43, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 71, 71, 71, 71, 71, 71, 71, 71, 71, 67, 43, 13, 7, 1, 1, 1, 1] 71
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 137
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057617 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057617
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057617/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057617
Building REAL300000057618
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057618'
/scratch/stefan/7769638/working/building/REAL300000057618 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057618

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057618/0 /scratch/stefan/7769638/working/building/REAL300000057618 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 647)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/647
`/scratch/stefan/7769638/working/3D/647' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Br)SC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057618.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057618.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057618/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057618 none CC1=C(Br)SC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 2, 2, 2, 7, 15, 37, 37, 37, 37, 37] 37
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21] set([7, 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: 105
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057618 none CC1=C(Br)SC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 37, 37, 37, 26, 26, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 26, 8, 5, 1, 1, 1, 1] 37
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: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057618 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057618
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057618/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057618
Building REAL300000057619
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057619'
/scratch/stefan/7769638/working/building/REAL300000057619 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057619

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057619/0 /scratch/stefan/7769638/working/building/REAL300000057619 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 648)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/648
`/scratch/stefan/7769638/working/3D/648' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1C=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1)

`REAL300000057619.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057619.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057619/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057619 none CCCN1C=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [18, 9, 1, 1, 1, 1, 1, 12, 12, 12, 39, 39, 39, 96, 114, 114, 96, 96, 114, 114, 114, 114, 1, 1, 18, 18, 18, 18, 18, 9, 9, 1, 12, 12, 12, 39, 96, 114, 114, 114, 114] 196
rigid atoms, others: [2, 3, 4, 5, 6, 22, 23, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 471
number of broken/clashed sets: 138
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057619 none CCCN1C=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [196, 196, 114, 114, 114, 62, 62, 62, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 114, 114, 196, 196, 196, 196, 196, 196, 196, 114, 62, 62, 62, 17, 7, 1, 1, 1, 1] 196
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 555
number of broken/clashed sets: 138
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057619 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057619
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057619/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057619
Building REAL300000057620
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057620'
/scratch/stefan/7769638/working/building/REAL300000057620 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057620

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057620/0 /scratch/stefan/7769638/working/building/REAL300000057620 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 649)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/649
`/scratch/stefan/7769638/working/3D/649' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCOCC1)

`REAL300000057620.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057620.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057620/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057620 none CC(C)CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 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, 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: [36, 35, 37, 21, 21, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 58, 58, 58, 58, 58, 37, 37, 37, 37, 37, 37, 37, 35, 35, 7, 7, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58] 61
rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 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, 48])
total number of confs: 240
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057620 none CC(C)CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 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, 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: [18, 19, 19, 12, 1, 12, 12, 33, 33, 33, 53, 58, 58, 53, 53, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 33, 53, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 1] 61
rigid atoms, others: [4, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 244
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057620 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057620
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057620/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057620
Building REAL300000057621
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057621'
/scratch/stefan/7769638/working/building/REAL300000057621 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057621

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057621/0 /scratch/stefan/7769638/working/building/REAL300000057621 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 650)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/650
`/scratch/stefan/7769638/working/3D/650' -> `0.mol2'
Preparing input files

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

`REAL300000057621.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057621.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057621/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057621 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Cl)=NC=C2C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 1, 7, 7, 6, 6, 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, 3, 7, 7, 7, 2, 2, 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, 8, 16, 16, 16, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 8, 16, 21, 25, 25, 1, 1] 25
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 33, 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])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057621 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Cl)=NC=C2C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 1, 7, 7, 6, 6, 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, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 6, 4, 1, 1, 7, 7] 7
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 23
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057621 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057621
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057621/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057621
Building REAL300000057622
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057622'
/scratch/stefan/7769638/working/building/REAL300000057622 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057622

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057622/0 /scratch/stefan/7769638/working/building/REAL300000057622 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 651)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/651
`/scratch/stefan/7769638/working/3D/651' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=CC3=C2CCCC3)C=C1)

`REAL300000057622.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057622.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057622/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057622 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=CC3=C2CCCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 13, 13, 13, 32, 32, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 9, 13, 32, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 41, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057622 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=CC3=C2CCCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 61, 62, 62, 61, 33, 33, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 61, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62] 62
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 41, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 174
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057622 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057622
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057622/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057622
Building REAL300000057623
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057623'
/scratch/stefan/7769638/working/building/REAL300000057623 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057623

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057623/0 /scratch/stefan/7769638/working/building/REAL300000057623 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 652)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/652
`/scratch/stefan/7769638/working/3D/652' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C3COCCN23)C=C1)

`REAL300000057623.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057623.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057623/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057623 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C3COCCN23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 12, 5, 5, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 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, 8, 10, 10, 10, 21, 21, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 8, 10, 21, 32, 32, 32, 32, 32, 32, 32, 1, 1] 32
rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 37, 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, 35])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057623 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C3COCCN23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 12, 5, 5, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 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, 17, 17, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 17, 8, 1, 1, 1, 1, 1, 1, 1, 32, 32] 32
rigid atoms, others: [32, 33, 34, 35, 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, 22, 23, 24, 25, 26, 27, 28, 37, 36])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057623 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057623
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057623/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057623
Building REAL300000057624
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057624'
/scratch/stefan/7769638/working/building/REAL300000057624 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057624

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057624/0 /scratch/stefan/7769638/working/building/REAL300000057624 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 653)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/653
`/scratch/stefan/7769638/working/3D/653' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Cl)

`REAL300000057624.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057624.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057624/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057624 none CC1=NN(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 13, 13, 35, 35, 35, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 2, 2, 2, 2, 2, 2, 13, 35, 59, 59, 59, 59, 59] 59
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057624 none CC1=NN(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 30, 30, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 30, 14, 7, 1, 1, 1, 1] 59
rigid atoms, others: [32, 33, 34, 35, 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])
total number of confs: 102
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057624 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057624
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057624/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057624
Building REAL300000057625
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057625'
/scratch/stefan/7769638/working/building/REAL300000057625 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057625

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057625/0 /scratch/stefan/7769638/working/building/REAL300000057625 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 654)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/654
`/scratch/stefan/7769638/working/3D/654' -> `0.mol2'
Preparing input files

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

`REAL300000057625.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057625.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057625/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057625 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(O)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 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]
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: [19, 19, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 41, 41, 30, 41, 41, 41, 41, 19, 19, 19, 15, 7, 1, 1, 1, 1, 41, 41, 82, 41] 82
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 217
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057625 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(O)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 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]
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: [7, 1, 7, 7, 21, 21, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 41, 41, 41, 41, 41, 1, 1, 2, 1] 82
rigid atoms, others: [1, 34, 36, 33, 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, 35])
total number of confs: 113
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057625 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057625
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057625/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057625
Building REAL300000057626
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057626'
/scratch/stefan/7769638/working/building/REAL300000057626 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057626

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057626/0 /scratch/stefan/7769638/working/building/REAL300000057626 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 655)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/655
`/scratch/stefan/7769638/working/3D/655' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(C2=NC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CS2)=N1)

`REAL300000057626.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057626.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057626/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057626 none CN1C=CC(C2=NC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CS2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 32, 32, 50, 50, 50, 78, 83, 83, 83, 83, 83, 83, 83, 83, 10, 10, 1, 2, 2, 2, 1, 1, 32, 50, 78, 83, 83, 83, 83, 10] 83
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 231
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057626 none CN1C=CC(C2=NC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CS2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 59, 66, 66, 65, 66, 66, 66, 66, 66, 1, 1, 10, 11, 11, 11, 10, 10, 9, 25, 59, 66, 66, 66, 66, 1] 83
rigid atoms, others: [4, 5, 6, 7, 8, 23, 24, 38] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 205
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057626 none CN1C=CC(C2=NC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CS2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 83, 83, 66, 66, 66, 36, 36, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 83, 83, 83, 83, 83, 83, 36, 12, 7, 1, 1, 1, 1, 66] 83
rigid atoms, others: [34, 35, 36, 37, 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, 38])
total number of confs: 139
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057626 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057626
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057626/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057626
Building REAL300000057627
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057627'
/scratch/stefan/7769638/working/building/REAL300000057627 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057627

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057627/0 /scratch/stefan/7769638/working/building/REAL300000057627 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 656)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/656
`/scratch/stefan/7769638/working/3D/656' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CCCC2)=N1)

`REAL300000057627.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057627.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057627/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057627 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CCCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 39, 40, 40, 106, 110, 110, 106, 109, 110, 110, 110, 110, 1, 1, 7, 7, 7, 7, 1, 2, 2, 2, 1, 12, 39, 106, 110, 110, 110, 110, 7, 7, 7, 7, 7, 7, 7, 7, 7] 180
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 340
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057627 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CCCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 110, 43, 43, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 110, 110, 180, 180, 180, 180, 110, 110, 110, 110, 110, 43, 13, 7, 1, 1, 1, 1, 180, 180, 180, 180, 180, 180, 180, 180, 180] 180
rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 394
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057627 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CCCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 41, 41, 97, 97, 97, 179, 180, 180, 179, 180, 180, 180, 180, 180, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8, 7, 41, 97, 179, 180, 180, 180, 180, 1, 1, 1, 1, 1, 1, 1, 1, 1] 180
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 517
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057627 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057627
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057627/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057627
Building REAL300000057628
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057628'
/scratch/stefan/7769638/working/building/REAL300000057628 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057628

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057628/0 /scratch/stefan/7769638/working/building/REAL300000057628 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 657)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/657
`/scratch/stefan/7769638/working/3D/657' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21)

`REAL300000057628.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057628.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057628/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057628 none COC1=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21 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.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', '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, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 12, 59, 59, 59, 130, 136, 136, 134, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 13, 13, 13, 59, 130, 136, 136, 136, 136, 1, 1, 1, 1, 1] 136
rigid atoms, others: [1, 2, 3, 4, 5, 41, 42, 43, 44, 45, 21, 22, 23, 24, 25, 26, 27, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 384
number of broken/clashed sets: 89
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057628 none COC1=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21 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.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', '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, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [136, 136, 136, 136, 49, 49, 49, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 49, 49, 49, 15, 7, 1, 1, 1, 1, 136, 136, 136, 136, 136] 136
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45])
total number of confs: 205
number of broken/clashed sets: 89
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057628 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057628
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057628/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057628
Building REAL300000057629
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057629'
/scratch/stefan/7769638/working/building/REAL300000057629 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057629

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057629/0 /scratch/stefan/7769638/working/building/REAL300000057629 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 658)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/658
`/scratch/stefan/7769638/working/3D/658' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Br)

`REAL300000057629.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057629.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057629/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057629 none CC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 1, 8, 8, 18, 18, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 2, 2, 2, 1, 1, 1, 8, 18, 36, 36, 36, 36, 36] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057629 none CC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 35, 36, 36, 30, 30, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 30, 12, 7, 1, 1, 1, 1] 36
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057629 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057629
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057629/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057629
Building REAL300000057630
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057630'
/scratch/stefan/7769638/working/building/REAL300000057630 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057630

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057630/0 /scratch/stefan/7769638/working/building/REAL300000057630 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 659)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/659
`/scratch/stefan/7769638/working/3D/659' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)C=C1)

`REAL300000057630.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057630.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057630/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057630 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 42, 42, 42, 42, 42, 167, 201, 201, 201, 201, 201, 201, 42, 1, 1, 1, 1, 6, 6, 14, 42, 42, 42, 201, 201, 201, 201, 42, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 296
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057630 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 42, 45, 41, 45, 45, 35, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 45, 45, 45, 45, 35, 15, 7, 1, 1, 1, 19, 19, 19, 19, 1, 45, 45] 201
rigid atoms, others: [34, 35, 36, 41, 12, 13, 14, 15, 16, 17, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 42, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057630 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 196, 114, 114, 114, 78, 78, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 196, 114, 78, 19, 19, 19, 1, 1, 1, 1, 19, 201, 201] 201
rigid atoms, others: [37, 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, 41, 42, 43])
total number of confs: 580
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057630 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057630
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057630/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057630
Building REAL300000057631
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057631'
/scratch/stefan/7769638/working/building/REAL300000057631 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057631

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057631/0 /scratch/stefan/7769638/working/building/REAL300000057631 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 660)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/660
`/scratch/stefan/7769638/working/3D/660' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OCCCC3=C2)C=C1)

`REAL300000057631.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057631.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057631/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057631 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OCCCC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 3, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 9
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057631 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3OCCCC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 22, 21, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 45
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 23, 24, 25, 26, 27, 28, 29, 39])
total number of confs: 121
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057631 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057631
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057631/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057631
Building REAL300000057632
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057632'
/scratch/stefan/7769638/working/building/REAL300000057632 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057632

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057632/0 /scratch/stefan/7769638/working/building/REAL300000057632 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 661)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/661
`/scratch/stefan/7769638/working/3D/661' -> `0.mol2'
Preparing input files

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

`REAL300000057632.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057632.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057632/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057632 none CN(C)C(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [13, 11, 13, 1, 11, 1, 1, 1, 1, 1, 1, 12, 12, 34, 35, 35, 60, 63, 63, 62, 62, 63, 63, 63, 63, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 12, 34, 60, 63, 63, 63, 63, 1] 141
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 25, 42] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 204
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057632 none CN(C)C(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 63, 141, 63, 63, 63, 63, 32, 32, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 63, 141, 141, 141, 141, 141, 141, 63, 63, 63, 32, 12, 7, 1, 1, 1, 1, 63] 141
rigid atoms, others: [38, 39, 40, 41, 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, 36, 37, 42])
total number of confs: 342
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057632 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057632
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057632/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057632
Building REAL300000057633
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057633'
/scratch/stefan/7769638/working/building/REAL300000057633 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057633

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057633/0 /scratch/stefan/7769638/working/building/REAL300000057633 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 662)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/662
`/scratch/stefan/7769638/working/3D/662' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1CC1CCC1)

`REAL300000057633.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057633/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057633 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 95, 95, 95, 95, 95, 165, 201, 201, 201, 30, 30, 30, 13, 7, 1, 1, 1, 1, 95, 95, 165, 165, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 651
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057633 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 33, 33, 76, 95, 95, 86, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 10, 10, 10, 33, 76, 95, 95, 95, 95, 1, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21] 201
rigid atoms, others: [1, 35, 36, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 351
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057633 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 73, 73, 118, 118, 118, 199, 201, 201, 201, 201, 201, 201, 201, 201, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 73, 73, 73, 118, 199, 201, 201, 201, 201, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 587
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057633 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057633
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057633/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057633
Building REAL300000057634
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057634'
/scratch/stefan/7769638/working/building/REAL300000057634 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057634

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057634/0 /scratch/stefan/7769638/working/building/REAL300000057634 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 663)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/663
`/scratch/stefan/7769638/working/3D/663' -> `0.mol2'
Preparing input files

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

`REAL300000057634.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057634.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057634/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057634 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(O)=CC(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 15, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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, 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: [30, 30, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 69, 69, 69, 69, 69, 69, 69, 30, 30, 30, 14, 7, 1, 1, 1, 1, 69, 138, 69, 69] 138
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 259
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057634 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(O)=CC(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 15, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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, 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: [11, 1, 11, 11, 41, 41, 41, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 41, 69, 69, 69, 69, 69, 1, 2, 1, 1] 138
rigid atoms, others: [1, 35, 36, 33, 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, 34])
total number of confs: 193
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057634 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057634
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057634/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057634
Building REAL300000057635
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057635'
/scratch/stefan/7769638/working/building/REAL300000057635 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057635

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057635/0 /scratch/stefan/7769638/working/building/REAL300000057635 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 664)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/664
`/scratch/stefan/7769638/working/3D/664' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057635.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057635.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057635/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057635 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 17, 17, 36, 37, 37, 36, 37, 37, 37, 37, 37, 2, 2, 2, 1, 6, 16, 36, 37, 37, 37, 37] 37
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])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057635 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 32, 32, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 32, 16, 7, 1, 1, 1, 1] 37
rigid atoms, others: [32, 33, 34, 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: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057635 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057635
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057635/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057635
Building REAL300000057636
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057636'
/scratch/stefan/7769638/working/building/REAL300000057636 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057636

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057636/0 /scratch/stefan/7769638/working/building/REAL300000057636 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 665)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/665
`/scratch/stefan/7769638/working/3D/665' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057636.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057636.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057636/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057636 none CSC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 14, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 33, 38, 38, 33, 35, 38, 38, 38, 38, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 33, 38, 38, 38, 38, 1, 1] 60
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 38, 39, 21, 25, 26, 27, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 32, 33, 34, 35, 36, 37])
total number of confs: 127
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057636 none CSC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 14, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [60, 38, 38, 38, 38, 38, 38, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 60, 60, 60, 38, 38, 38, 38, 38, 38, 38, 13, 7, 1, 1, 1, 1, 38, 38] 60
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 110
number of broken/clashed sets: 35
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057636 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057636
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057636/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057636
Building REAL300000057637
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057637'
/scratch/stefan/7769638/working/building/REAL300000057637 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057637

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057637/0 /scratch/stefan/7769638/working/building/REAL300000057637 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 666)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/666
`/scratch/stefan/7769638/working/3D/666' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1S(N)(=O)=O)

`REAL300000057637.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057637.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057637/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057637 none CN1N=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1S(N)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 8, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 6, 6, 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, 4, 4, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 4, 4, 4, 2, 2, 2, 1, 4, 6, 12, 12, 12, 12, 12, 4, 4] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 53
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057637 none CN1N=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1S(N)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 8, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 6, 6, 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: [12, 12, 12, 12, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 13, 13, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 13, 13] 13
rigid atoms, others: [32, 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, 36, 37])
total number of confs: 28
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057637 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057637
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057637/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057637
Building REAL300000057638
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057638'
/scratch/stefan/7769638/working/building/REAL300000057638 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057638

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057638/0 /scratch/stefan/7769638/working/building/REAL300000057638 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 667)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/667
`/scratch/stefan/7769638/working/3D/667' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C3CC3)NN=C2Cl)C=C1)

`REAL300000057638.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057638.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057638/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057638 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C3CC3)NN=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 16, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 18, 18, 18, 45, 45, 115, 115, 142, 142, 115, 115, 115, 115, 1, 1, 1, 1, 12, 18, 45, 142, 142, 142, 142, 142, 115, 1, 1] 142
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 36] set([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: 285
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057638 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C3CC3)NN=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 16, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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: [122, 122, 122, 116, 122, 122, 112, 46, 46, 46, 12, 12, 1, 1, 1, 1, 7, 7, 1, 1, 1, 1, 122, 122, 122, 122, 112, 45, 12, 7, 7, 7, 7, 7, 1, 122, 122] 148
rigid atoms, others: [34, 12, 13, 14, 15, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 361
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057638 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(C3CC3)NN=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 16, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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, 148, 148, 148, 88, 88, 88, 44, 44, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 148, 148, 148, 148, 148, 88, 44, 1, 1, 1, 1, 1, 7, 148, 148] 148
rigid atoms, others: [32, 33, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 398
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057638 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057638
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057638/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057638
Building REAL300000057639
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057639'
/scratch/stefan/7769638/working/building/REAL300000057639 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057639

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057639/0 /scratch/stefan/7769638/working/building/REAL300000057639 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 668)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/668
`/scratch/stefan/7769638/working/3D/668' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=NO1)

`REAL300000057639.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057639.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057639/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057639 none CCC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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: [5, 1, 1, 1, 1, 12, 12, 42, 43, 43, 97, 109, 109, 103, 109, 109, 109, 109, 109, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 42, 97, 109, 109, 109, 109, 2, 2, 2] 136
rigid atoms, others: [1, 2, 3, 4, 19, 20, 21, 22] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 331
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057639 none CCC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [136, 109, 109, 56, 56, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 109, 109, 109, 109, 136, 136, 136, 136, 136, 56, 16, 7, 1, 1, 1, 1, 109, 109, 109] 136
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37])
total number of confs: 348
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057639 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057639
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057639/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057639
Building REAL300000057640
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057640'
/scratch/stefan/7769638/working/building/REAL300000057640 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057640

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057640/0 /scratch/stefan/7769638/working/building/REAL300000057640 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 669)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/669
`/scratch/stefan/7769638/working/3D/669' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(CC2CCC2)N=C1)

`REAL300000057640.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057640.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057640/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057640 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(CC2CCC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 22, 87, 87, 87, 165, 201, 201, 201, 87, 87, 22, 22, 22, 10, 7, 1, 1, 1, 1, 87, 165, 165, 201, 201, 201, 201, 201, 201, 201, 87] 201
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 642
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057640 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(CC2CCC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 35, 36, 36, 73, 87, 87, 82, 87, 87, 87, 87, 87, 1, 1, 1, 1, 9, 30, 30, 30, 1, 1, 13, 13, 13, 35, 73, 87, 87, 87, 87, 1, 9, 9, 30, 30, 30, 30, 30, 30, 30, 1] 201
rigid atoms, others: [1, 35, 45, 16, 17, 18, 19, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 357
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057640 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(CC2CCC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [116, 30, 116, 116, 155, 155, 155, 198, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30, 6, 1, 1, 1, 1, 1, 30, 30, 116, 116, 116, 155, 198, 201, 201, 201, 201, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 30] 201
rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 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, 37, 45])
total number of confs: 566
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057640 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057640
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057640/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057640
Building REAL300000057641
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057641'
/scratch/stefan/7769638/working/building/REAL300000057641 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057641

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057641/0 /scratch/stefan/7769638/working/building/REAL300000057641 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 670)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/670
`/scratch/stefan/7769638/working/3D/670' -> `0.mol2'
Preparing input files

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

`REAL300000057641.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057641.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057641/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057641 none CN(C)C1=NC(C(F)(F)F)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 5, 1, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 2, 2, 2, 1, 1, 1, 1, 6, 6, 16, 16, 16, 35, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 3, 3, 1, 1, 6, 16, 35, 36, 36, 36, 36] 36
rigid atoms, others: [1, 34, 3, 4, 5, 6, 10, 11, 12, 13, 35] set([0, 2, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 105
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057641 none CN(C)C1=NC(C(F)(F)F)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 5, 1, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 36, 36, 36, 26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 26, 14, 7, 1, 1, 1, 1] 36
rigid atoms, others: [39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057641 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057641
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057641/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057641
Building REAL300000057642
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057642'
/scratch/stefan/7769638/working/building/REAL300000057642 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057642

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057642/0 /scratch/stefan/7769638/working/building/REAL300000057642 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 671)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/671
`/scratch/stefan/7769638/working/3D/671' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1)

`REAL300000057642.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057642.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057642/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057642 none CCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [8, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 45, 47, 47, 45, 45, 47, 47, 47, 47, 1, 1, 8, 8, 8, 8, 8, 1, 7, 22, 45, 47, 47, 47, 47] 73
rigid atoms, others: [1, 2, 3, 4, 5, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057642 none CCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 47, 47, 47, 34, 34, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 47, 47, 73, 73, 73, 73, 73, 47, 34, 13, 7, 1, 1, 1, 1] 73
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 250
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057642 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057642
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057642/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057642
Building REAL300000057643
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057643'
/scratch/stefan/7769638/working/building/REAL300000057643 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057643

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057643/0 /scratch/stefan/7769638/working/building/REAL300000057643 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 672)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/672
`/scratch/stefan/7769638/working/3D/672' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC([N+](=O)[O-])=C1)

`REAL300000057643.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057643.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057643/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057643 none COC1=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC([N+](=O)[O-])=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 12, 12, 12, 42, 42, 42, 73, 85, 85, 78, 78, 85, 85, 85, 85, 1, 1, 1, 2, 2, 1, 3, 3, 3, 1, 13, 13, 13, 42, 73, 85, 85, 85, 85, 1, 1] 85
rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 21, 22, 23, 26, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 286
number of broken/clashed sets: 63
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057643 none COC1=CC(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC([N+](=O)[O-])=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 85, 38, 38, 38, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 38, 38, 38, 15, 7, 1, 1, 1, 1, 85, 85] 85
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 138
number of broken/clashed sets: 63
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057643 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057643
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057643/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057643
Building REAL300000057644
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057644'
/scratch/stefan/7769638/working/building/REAL300000057644 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057644

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057644/0 /scratch/stefan/7769638/working/building/REAL300000057644 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 673)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/673
`/scratch/stefan/7769638/working/3D/673' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057644.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057644.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057644/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057644 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 17, 17, 17, 36, 37, 37, 36, 37, 37, 37, 37, 37, 2, 2, 2, 1, 1, 7, 17, 36, 37, 37, 37, 37] 37
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])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057644 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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: [37, 37, 37, 37, 37, 37, 37, 37, 32, 32, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 32, 16, 7, 1, 1, 1, 1] 37
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])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057644 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057644
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057644/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057644
Building REAL300000057645
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057645'
/scratch/stefan/7769638/working/building/REAL300000057645 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057645

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057645/0 /scratch/stefan/7769638/working/building/REAL300000057645 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 674)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/674
`/scratch/stefan/7769638/working/3D/674' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1)

`REAL300000057645.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057645.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057645/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057645 none CC(C)CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 8, 32, 33, 33, 73, 84, 84, 77, 84, 84, 84, 84, 84, 1, 1, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 1, 8, 32, 73, 84, 84, 84, 84, 1] 141
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 43, 35, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 287
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057645 none CC(C)CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [134, 141, 141, 84, 84, 84, 84, 41, 41, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 84, 84, 141, 141, 141, 141, 141, 141, 141, 141, 141, 84, 84, 41, 14, 7, 1, 1, 1, 1, 84] 141
rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 494
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057645 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057645
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057645/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057645
Building REAL300000057646
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057646'
/scratch/stefan/7769638/working/building/REAL300000057646 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057646

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057646/0 /scratch/stefan/7769638/working/building/REAL300000057646 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 675)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/675
`/scratch/stefan/7769638/working/3D/675' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CC=C3)N2)C=C1)

`REAL300000057646.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057646.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057646/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057646 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CC=C3)N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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, 3, 5, 5, 5, 7, 7, 7, 7, 7, 7, 13, 13, 7, 13, 13, 7, 1, 1, 1, 1, 3, 5, 7, 7, 7, 13, 13, 7, 13, 13, 7, 1, 1] 13
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057646 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CC=C3)N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 47, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 49, 49, 49, 49, 47, 24, 7, 1, 1, 6, 6, 1, 6, 7, 1, 49, 49] 87
rigid atoms, others: [32, 38, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 39, 40])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057646 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3=CC=CC=C3)N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 56, 56, 56, 22, 22, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 87, 87, 87, 87, 87, 56, 22, 6, 6, 1, 1, 1, 1, 1, 6, 87, 87] 87
rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 247
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057646 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057646
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057646/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057646
Building REAL300000057647
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057647'
/scratch/stefan/7769638/working/building/REAL300000057647 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057647

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057647/0 /scratch/stefan/7769638/working/building/REAL300000057647 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 676)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/676
`/scratch/stefan/7769638/working/3D/676' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=N1)

`REAL300000057647.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057647/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057647 none CC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 21, 21, 21, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 1, 11, 21, 38, 38, 38, 38, 38, 2, 2, 2] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 117
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057647 none CC1=NC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 28, 28, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 38, 38, 38, 28, 12, 7, 1, 1, 1, 1, 38, 38, 38] 38
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 74
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057647 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057647
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057647/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057647
Building REAL300000057648
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057648'
/scratch/stefan/7769638/working/building/REAL300000057648 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057648

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057648/0 /scratch/stefan/7769638/working/building/REAL300000057648 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 677)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/677
`/scratch/stefan/7769638/working/3D/677' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CNC(N)=[NH+]1)

`REAL300000057648.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057648.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057648/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057648 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CNC(N)=[NH+]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'N.pl3', 'N.pl3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 16, 22, 22, 22, 22, 22, 22, 16, 16, 16, 6, 6, 1, 1, 1, 1, 22, 22, 22, 22] 22
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 43
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057648 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CNC(N)=[NH+]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'N.pl3', 'N.pl3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 4, 4, 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: [8, 1, 8, 8, 18, 19, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 22, 22, 22, 22, 22, 1, 1, 2, 2] 22
rigid atoms, others: [32, 1, 33, 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, 34, 35])
total number of confs: 71
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057648 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057648/1 /scratch/stefan/7769638/working/building/REAL300000057648 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 678)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/678
`/scratch/stefan/7769638/working/3D/678' -> `1.mol2'
Preparing input files

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

`REAL300000057648.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057648.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057648/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057648 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CNC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 18, 18, 18, 18, 18, 16, 16, 16, 10, 7, 1, 1, 1, 1, 18, 18, 18, 18] 18
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 34, 33, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 41
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057648 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CNC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [8, 1, 8, 8, 14, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 18, 18, 18, 18, 18, 1, 1, 1, 1] 18
rigid atoms, others: [32, 1, 34, 33, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 45
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057648 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057648
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057648/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057648/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057648
Building REAL300000057649
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057649'
/scratch/stefan/7769638/working/building/REAL300000057649 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057649

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057649/0 /scratch/stefan/7769638/working/building/REAL300000057649 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 679)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/679
`/scratch/stefan/7769638/working/3D/679' -> `0.mol2'
Preparing input files

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

`REAL300000057649.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057649.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057649/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057649 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 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]
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: [22, 22, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 22, 54, 54, 54, 54, 54, 54, 54, 22, 22, 22, 14, 7, 1, 1, 1, 1, 54, 54, 108, 54] 108
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 210
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057649 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', '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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 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]
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: [11, 1, 11, 11, 33, 34, 34, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 33, 54, 54, 54, 54, 54, 1, 1, 2, 1] 108
rigid atoms, others: [1, 34, 36, 33, 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, 35])
total number of confs: 151
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057649 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057649
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057649/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057649
Building REAL300000057650
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057650'
/scratch/stefan/7769638/working/building/REAL300000057650 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057650

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057650/0 /scratch/stefan/7769638/working/building/REAL300000057650 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 680)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/680
`/scratch/stefan/7769638/working/3D/680' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(C3=CC=CC=N3)=N2)C=C1)

`REAL300000057650.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057650.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057650/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057650 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(C3=CC=CC=N3)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 30, 30, 46, 46, 46, 46, 46, 88, 88, 88, 88, 88, 46, 1, 1, 1, 1, 8, 12, 30, 46, 46, 88, 88, 88, 88, 1, 1] 88
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 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])
total number of confs: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057650 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(C3=CC=CC=N3)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [46, 45, 46, 45, 46, 46, 44, 17, 16, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 1, 46, 46, 46, 46, 44, 16, 6, 1, 1, 13, 13, 12, 13, 46, 46] 88
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057650 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(C3=CC=CC=N3)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 54, 54, 54, 38, 38, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 88, 88, 88, 88, 88, 54, 38, 12, 13, 1, 1, 1, 1, 88, 88] 88
rigid atoms, others: [34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 247
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057650 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057650
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057650/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057650
Building REAL300000057651
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057651'
/scratch/stefan/7769638/working/building/REAL300000057651 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057651

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057651/0 /scratch/stefan/7769638/working/building/REAL300000057651 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 681)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/681
`/scratch/stefan/7769638/working/3D/681' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Br)N1)

`REAL300000057651.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057651.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057651/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057651 none CC1=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Br)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 22, 23, 23, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 2, 2, 2, 6, 22, 64, 64, 64, 64, 64, 1] 64
rigid atoms, others: [0, 1, 2, 3, 4, 32, 19, 20, 21] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057651 none CC1=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Br)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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]
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, 44, 44, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 64, 64, 64, 64, 64, 64, 44, 16, 7, 1, 1, 1, 1, 64] 64
rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 126
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057651 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057651/1 /scratch/stefan/7769638/working/building/REAL300000057651 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 682)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/682
`/scratch/stefan/7769638/working/3D/682' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(Br)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1)

`REAL300000057651.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057651.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057651/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057651 none CC1=NC(Br)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 6, 12, 22, 22, 22, 22, 22, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 21] set([7, 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: 59
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057651 none CC1=NC(Br)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 20, 20, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 20, 10, 7, 1, 1, 1, 1, 22] 22
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, 32, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 46
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057651 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057651
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057651/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057651/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057651
Building REAL300000057652
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057652'
/scratch/stefan/7769638/working/building/REAL300000057652 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057652

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057652/0 /scratch/stefan/7769638/working/building/REAL300000057652 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 683)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/683
`/scratch/stefan/7769638/working/3D/683' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CS(=O)(=O)C3)CC2)C=C1)

`REAL300000057652.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057652.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057652/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057652 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CS(=O)(=O)C3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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, 11, 8, 8, 1, 5, 5, 5, 5, 14, 11, 11, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 7, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 44
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057652 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CS(=O)(=O)C3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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, 11, 8, 8, 1, 5, 5, 5, 5, 14, 11, 11, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 21, 22, 21, 22, 22, 21, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 22
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 41, 23, 24, 25, 26, 27, 28])
total number of confs: 66
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057652 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057652
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057652/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057652
Building REAL300000057653
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057653'
/scratch/stefan/7769638/working/building/REAL300000057653 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057653

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057653/0 /scratch/stefan/7769638/working/building/REAL300000057653 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 684)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/684
`/scratch/stefan/7769638/working/3D/684' -> `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)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057653.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057653.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057653/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057653 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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
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, 2, 2, 1, 1, 1, 4, 4, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 10, 28, 28, 28, 28, 28] 28
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])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057653 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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
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, 20, 20, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 20, 12, 7, 1, 1, 1, 1] 28
rigid atoms, others: [39, 40, 41, 42, 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, 38])
total number of confs: 58
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057653 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057653
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057653/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057653
Building REAL300000057654
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057654'
/scratch/stefan/7769638/working/building/REAL300000057654 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057654

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057654/0 /scratch/stefan/7769638/working/building/REAL300000057654 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 685)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/685
`/scratch/stefan/7769638/working/3D/685' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C(=O)NC2=C1Cl)

`REAL300000057654.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057654.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057654/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057654 none CC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C(=O)NC2=C1Cl 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 6, 6, 19, 20, 20, 19, 19, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 19, 20, 20, 20, 20, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 29, 30, 37] set([32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 31])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057654 none CC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C(=O)NC2=C1Cl 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 18, 7, 1, 1, 1, 1, 20] 20
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057654 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057654
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057654/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057654
Building REAL300000057655
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057655'
/scratch/stefan/7769638/working/building/REAL300000057655 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057655

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057655/0 /scratch/stefan/7769638/working/building/REAL300000057655 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 686)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/686
`/scratch/stefan/7769638/working/3D/686' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C2CCCCC2=N1)

`REAL300000057655.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057655.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057655/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057655 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C2CCCCC2=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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, 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, 11, 11, 24, 24, 24, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 11, 24, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1] 52
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057655 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C2CCCCC2=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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, 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, 34, 34, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 34, 17, 7, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52] 52
rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057655 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057655
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057655/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057655
Building REAL300000057656
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057656'
/scratch/stefan/7769638/working/building/REAL300000057656 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057656

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057656/0 /scratch/stefan/7769638/working/building/REAL300000057656 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 687)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/687
`/scratch/stefan/7769638/working/3D/687' -> `0.mol2'
Preparing input files

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

`REAL300000057656.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057656.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057656/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057656 none COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [8, 8, 1, 8, 1, 1, 1, 1, 1, 6, 6, 11, 12, 12, 28, 34, 34, 28, 31, 34, 34, 34, 34, 1, 1, 9, 9, 9, 1, 1, 6, 11, 28, 34, 34, 34, 34, 1] 56
rigid atoms, others: [2, 4, 5, 6, 7, 8, 23, 24, 28, 29, 37] set([0, 1, 3, 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: 144
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057656 none COC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 34, 56, 34, 34, 34, 27, 27, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 34, 34, 56, 56, 56, 34, 34, 27, 10, 7, 1, 1, 1, 1, 34] 56
rigid atoms, others: [33, 34, 35, 36, 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, 37])
total number of confs: 143
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057656 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057656
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057656/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057656
Building REAL300000057657
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057657'
/scratch/stefan/7769638/working/building/REAL300000057657 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057657

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057657/0 /scratch/stefan/7769638/working/building/REAL300000057657 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 688)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/688
`/scratch/stefan/7769638/working/3D/688' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2N2CCCCC2)C=C1)

`REAL300000057657.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057657.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057657/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057657 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2N2CCCCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 5, 7, 7, 7, 7, 7, 11, 11, 7, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 5, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 46, 47, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 39
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057657 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2N2CCCCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 32, 33, 33, 32, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 33, 33, 33, 33, 32, 11, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 33, 33] 33
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057657 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2N2CCCCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 32, 11, 11, 11, 5, 5, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 32, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 33
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47])
total number of confs: 90
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057657 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057657
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057657/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057657
Building REAL300000057658
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057658'
/scratch/stefan/7769638/working/building/REAL300000057658 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057658

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057658/0 /scratch/stefan/7769638/working/building/REAL300000057658 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 689)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/689
`/scratch/stefan/7769638/working/3D/689' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CSC(C(F)(F)F)=N2)C=C1)

`REAL300000057658.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057658.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057658/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057658 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CSC(C(F)(F)F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 6, 6, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 28, 28, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 8, 12, 28, 37, 1, 1] 37
rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29])
total number of confs: 78
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057658 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CSC(C(F)(F)F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 6, 6, 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, 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, 19, 19, 19, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 39, 39, 39, 39, 39, 18, 8, 1, 39, 39] 39
rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 108
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057658 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057658
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057658/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057658
Building REAL300000057659
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057659'
/scratch/stefan/7769638/working/building/REAL300000057659 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057659

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057659/0 /scratch/stefan/7769638/working/building/REAL300000057659 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 690)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/690
`/scratch/stefan/7769638/working/3D/690' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057659.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057659.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057659/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057659 none CCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 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, 2, 2, 7, 7, 3, 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: [18, 8, 1, 1, 1, 1, 1, 1, 6, 6, 22, 23, 23, 57, 66, 66, 63, 66, 66, 66, 66, 66, 1, 18, 18, 18, 18, 18, 1, 1, 6, 22, 57, 66, 66, 66, 66] 91
rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 240
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057659 none CCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 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, 2, 2, 7, 7, 3, 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, 89, 66, 66, 66, 66, 44, 44, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 66, 91, 91, 91, 91, 91, 66, 66, 44, 16, 7, 1, 1, 1, 1] 91
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 168
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057659 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057659
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057659/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057659
Building REAL300000057660
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057660'
/scratch/stefan/7769638/working/building/REAL300000057660 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057660

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057660/0 /scratch/stefan/7769638/working/building/REAL300000057660 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 691)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/691
`/scratch/stefan/7769638/working/3D/691' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057660.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057660.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057660/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057660 none CCN1C=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 2, 2, 2, 2, 2, 1, 7, 12, 30, 30, 30, 30, 30, 1] 59
rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 21, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057660 none CCN1C=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 30, 30, 30, 30, 24, 24, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 59, 59, 59, 59, 59, 30, 24, 8, 5, 1, 1, 1, 1, 30] 59
rigid atoms, others: [32, 33, 34, 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, 35])
total number of confs: 230
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057660 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057660
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057660/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057660
Building REAL300000057661
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057661'
/scratch/stefan/7769638/working/building/REAL300000057661 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057661

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057661/0 /scratch/stefan/7769638/working/building/REAL300000057661 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 692)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/692
`/scratch/stefan/7769638/working/3D/692' -> `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)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057661.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057661.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057661/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057661 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 18, 19, 19, 31, 37, 37, 35, 37, 37, 37, 37, 37, 1, 2, 2, 2, 1, 6, 18, 31, 37, 37, 37, 37] 37
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])
total number of confs: 118
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057661 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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, 37, 30, 30, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 30, 10, 6, 1, 1, 1, 1] 37
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057661 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057661
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057661/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057661
Building REAL300000057662
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057662'
/scratch/stefan/7769638/working/building/REAL300000057662 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057662

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057662/0 /scratch/stefan/7769638/working/building/REAL300000057662 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 693)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/693
`/scratch/stefan/7769638/working/3D/693' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN=C1F)

`REAL300000057662.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057662.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057662/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057662 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 2, 2, 2, 1, 7, 21, 49, 49, 49, 49, 49, 1] 49
rigid atoms, others: [0, 1, 2, 3, 4, 34, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057662 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CN=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 28, 28, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 28, 12, 7, 1, 1, 1, 1, 49] 49
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, 34, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057662 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057662
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057662/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057662
Building REAL300000057663
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057663'
/scratch/stefan/7769638/working/building/REAL300000057663 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057663

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057663/0 /scratch/stefan/7769638/working/building/REAL300000057663 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 694)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/694
`/scratch/stefan/7769638/working/3D/694' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(F)=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057663.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057663.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057663/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057663 none CC1=CC(F)=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 15, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 1, 1, 1, 13, 13, 23, 23, 23, 36, 36, 36, 36, 36, 36, 36, 36, 36, 2, 2, 2, 1, 1, 13, 23, 36, 36, 36, 36, 36] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057663 none CC1=CC(F)=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 15, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 22, 22, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 36, 36, 36, 36, 22, 10, 7, 1, 1, 1, 1] 36
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057663 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057663
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057663/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057663
Building REAL300000057664
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057664'
/scratch/stefan/7769638/working/building/REAL300000057664 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057664

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057664/0 /scratch/stefan/7769638/working/building/REAL300000057664 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 695)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/695
`/scratch/stefan/7769638/working/3D/695' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)F)C(F)=C2)C=C1)

`REAL300000057664.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057664.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057664/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057664 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)F)C(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 19, 19, 19, 43, 43, 91, 91, 91, 91, 107, 107, 91, 91, 91, 1, 1, 1, 1, 8, 19, 43, 91, 91, 107, 91, 1, 1] 107
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: 263
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057664 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(F)F)C(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 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, 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: [84, 82, 84, 75, 84, 84, 75, 30, 30, 30, 10, 10, 1, 1, 1, 1, 1, 1, 10, 10, 1, 1, 1, 84, 84, 84, 84, 75, 30, 10, 1, 1, 10, 1, 84, 84] 96
rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 34, 35])
total number of confs: 298
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057664 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057664
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057664/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057664
Building REAL300000057665
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057665'
/scratch/stefan/7769638/working/building/REAL300000057665 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057665

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057665/0 /scratch/stefan/7769638/working/building/REAL300000057665 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 696)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/696
`/scratch/stefan/7769638/working/3D/696' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3COCCC3C2)C=C1)

`REAL300000057665.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057665.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057665/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057665 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3COCCC3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 12, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 15, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 8, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1] 26
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 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, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 66
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057665 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3COCCC3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 12, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 26, 26, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 26
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 43, 22, 23, 24, 25, 26, 27])
total number of confs: 65
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057665 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057665
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057665/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057665
Building REAL300000057666
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057666'
/scratch/stefan/7769638/working/building/REAL300000057666 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057666

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057666/0 /scratch/stefan/7769638/working/building/REAL300000057666 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 697)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/697
`/scratch/stefan/7769638/working/3D/697' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1)

`REAL300000057666.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057666.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057666/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057666 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 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, 7, 4, 7, 6, 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]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 13, 13, 29, 29, 29, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 3, 3, 3, 1, 1, 13, 29, 69, 69, 69, 69, 69, 2, 2, 2, 1] 69
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 21, 22, 23, 27, 28] set([0, 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])
total number of confs: 196
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057666 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 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, 7, 4, 7, 6, 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]
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, 36, 37, 69, 69, 35, 35, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 35, 15, 7, 1, 1, 1, 1, 69, 69, 69, 69] 69
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 213
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057666 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057666
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057666/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057666
Building REAL300000057667
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057667'
/scratch/stefan/7769638/working/building/REAL300000057667 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057667

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057667/0 /scratch/stefan/7769638/working/building/REAL300000057667 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 698)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/698
`/scratch/stefan/7769638/working/3D/698' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Cl)C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Cl)

`REAL300000057667.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057667.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057667/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057667 none CC1=C(Cl)C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 1, 1, 8, 8, 18, 18, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 2, 2, 2, 1, 1, 8, 18, 32, 32, 32, 32, 32] 32
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057667 none CC1=C(Cl)C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 31, 32, 32, 32, 26, 26, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 32, 26, 12, 7, 1, 1, 1, 1] 32
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 69
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057667 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057667
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057667/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057667
Building REAL300000057668
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057668'
/scratch/stefan/7769638/working/building/REAL300000057668 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057668

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057668/0 /scratch/stefan/7769638/working/building/REAL300000057668 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 699)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/699
`/scratch/stefan/7769638/working/3D/699' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(Br)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057668.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057668.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057668/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057668 none N#CC1=CC=C(Br)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 10, 22, 40, 40, 40, 40, 40, 1] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057668 none N#CC1=CC=C(Br)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 30, 30, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 30, 12, 7, 1, 1, 1, 1, 40] 40
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057668 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057668
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057668/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057668
Building REAL300000057669
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057669'
/scratch/stefan/7769638/working/building/REAL300000057669 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057669

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057669/0 /scratch/stefan/7769638/working/building/REAL300000057669 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 700)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/700
`/scratch/stefan/7769638/working/3D/700' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC2=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC=C2O1)

`REAL300000057669.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057669.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057669/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057669 none CC1CC2=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 20, 45, 45, 45, 45, 45, 1, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 21, 22, 23, 24, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 126
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057669 none CC1CC2=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 25, 25, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 25, 10, 6, 1, 1, 1, 1, 45, 45] 45
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057669 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057669
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057669/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057669
Building REAL300000057670
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057670'
/scratch/stefan/7769638/working/building/REAL300000057670 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057670

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057670/0 /scratch/stefan/7769638/working/building/REAL300000057670 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 701)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/701
`/scratch/stefan/7769638/working/3D/701' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2OC(=O)N3)C=C1)

`REAL300000057670.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057670.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057670/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057670 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2OC(=O)N3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.2', 'O.2', 'N.am', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 14, 14, 30, 30, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 8, 14, 30, 41, 41, 41, 41, 1, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 23, 24, 25, 26] set([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: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057670 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2OC(=O)N3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.2', 'O.2', 'N.am', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 46, 21, 21, 21, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 46, 21, 11, 1, 1, 1, 1, 47, 47] 47
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057670 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057670
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057670/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057670
Building REAL300000057671
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057671'
/scratch/stefan/7769638/working/building/REAL300000057671 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057671

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057671/0 /scratch/stefan/7769638/working/building/REAL300000057671 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 702)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/702
`/scratch/stefan/7769638/working/3D/702' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2OCC3)C=C1)

`REAL300000057671.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057671.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057671/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057671 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2OCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 21, 21, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 8, 13, 21, 26, 26, 26, 26, 26, 26, 26, 1, 1] 26
rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 37, 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, 35])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057671 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2OCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.3', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 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, 15, 14, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 14, 9, 1, 1, 1, 1, 1, 1, 1, 29, 29] 29
rigid atoms, others: [32, 33, 34, 35, 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, 22, 23, 24, 25, 26, 27, 28, 37, 36])
total number of confs: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057671 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057671
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057671/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057671
Building REAL300000057672
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057672'
/scratch/stefan/7769638/working/building/REAL300000057672 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057672

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057672/0 /scratch/stefan/7769638/working/building/REAL300000057672 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 703)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/703
`/scratch/stefan/7769638/working/3D/703' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000057672.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057672.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057672/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057672 none CSCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 14, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [16, 4, 1, 1, 1, 1, 1, 1, 8, 8, 26, 27, 27, 61, 67, 67, 65, 67, 67, 67, 67, 67, 1, 1, 16, 16, 16, 4, 4, 1, 1, 8, 26, 61, 67, 67, 67, 67, 1, 1] 121
rigid atoms, others: [2, 3, 4, 5, 6, 7, 39, 22, 23, 38, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057672 none CSCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 14, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [121, 71, 53, 32, 67, 67, 32, 32, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 119, 121, 121, 71, 71, 67, 67, 32, 14, 7, 1, 1, 1, 1, 67, 67] 121
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, 38, 39])
total number of confs: 400
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057672 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057672
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057672/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057672
Building REAL300000057673
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057673'
/scratch/stefan/7769638/working/building/REAL300000057673 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057673

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057673/0 /scratch/stefan/7769638/working/building/REAL300000057673 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 704)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/704
`/scratch/stefan/7769638/working/3D/704' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCC3)N=C2)C=C1)

`REAL300000057673.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057673.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057673/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057673 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.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, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 28, 68, 68, 68, 151, 201, 201, 201, 68, 68, 1, 1, 1, 1, 7, 7, 28, 68, 151, 151, 201, 201, 201, 201, 201, 201, 201, 68, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 689
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057673 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.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, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 61, 66, 66, 55, 25, 24, 25, 6, 6, 1, 1, 1, 1, 1, 9, 31, 31, 31, 1, 1, 66, 66, 66, 66, 55, 24, 6, 1, 9, 9, 31, 31, 31, 31, 31, 31, 31, 1, 66, 66] 201
rigid atoms, others: [40, 12, 13, 14, 15, 16, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42])
total number of confs: 291
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057673 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CCC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.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, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 199, 142, 142, 142, 91, 91, 31, 31, 31, 6, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 199, 142, 91, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 31, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42])
total number of confs: 573
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057673 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057673
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057673/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057673
Building REAL300000057674
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057674'
/scratch/stefan/7769638/working/building/REAL300000057674 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057674

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057674/0 /scratch/stefan/7769638/working/building/REAL300000057674 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 705)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/705
`/scratch/stefan/7769638/working/3D/705' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C2CCOCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057674.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057674.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057674/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057674 none CN1N=C2CCOCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 12, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 28, 28, 47, 49, 49, 47, 49, 49, 49, 49, 49, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 27, 47, 49, 49, 49, 49] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 145
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057674 none CN1N=C2CCOCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 12, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 33, 33, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 33, 14, 7, 1, 1, 1, 1] 49
rigid atoms, others: [37, 38, 39, 40, 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, 36])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057674 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057674
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057674/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057674
Building REAL300000057675
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057675'
/scratch/stefan/7769638/working/building/REAL300000057675 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057675

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057675/0 /scratch/stefan/7769638/working/building/REAL300000057675 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 706)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/706
`/scratch/stefan/7769638/working/3D/706' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C2CCCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057675.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057675/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057675 none CN1N=C2CCCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 10, 10, 25, 25, 25, 41, 41, 41, 41, 41, 41, 41, 41, 41, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 24, 41, 41, 41, 41, 41] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057675 none CN1N=C2CCCC2=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 14, 7, 1, 1, 1, 1] 41
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 86
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057675 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057675
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057675/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057675
Building REAL300000057676
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057676'
/scratch/stefan/7769638/working/building/REAL300000057676 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057676

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057676/0 /scratch/stefan/7769638/working/building/REAL300000057676 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 707)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/707
`/scratch/stefan/7769638/working/3D/707' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCC2)C=C1)

`REAL300000057676.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057676.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057676/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057676 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 19, 19, 19, 51, 51, 114, 114, 114, 114, 114, 162, 162, 162, 1, 1, 1, 1, 10, 19, 51, 114, 114, 162, 162, 162, 162, 162, 162, 162, 1, 1] 162
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 368
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057676 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [102, 102, 102, 96, 102, 102, 91, 33, 33, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 102, 102, 102, 102, 91, 33, 10, 1, 1, 8, 8, 8, 8, 8, 8, 8, 102, 102] 146
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057676 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NN2C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [146, 146, 146, 146, 146, 146, 146, 68, 68, 68, 33, 33, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 68, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 146, 146] 146
rigid atoms, others: [32, 33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39])
total number of confs: 411
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057676 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057676
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057676/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057676
Building REAL300000057677
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057677'
/scratch/stefan/7769638/working/building/REAL300000057677 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057677

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057677/0 /scratch/stefan/7769638/working/building/REAL300000057677 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 708)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/708
`/scratch/stefan/7769638/working/3D/708' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCC3)N=C2)C=C1)

`REAL300000057677.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057677.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057677/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057677 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 11, 20, 20, 20, 67, 67, 126, 126, 126, 201, 201, 201, 126, 126, 1, 1, 1, 1, 11, 20, 67, 126, 201, 201, 201, 201, 201, 201, 201, 126, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 470
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057677 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [124, 124, 124, 115, 124, 124, 108, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 124, 124, 124, 124, 108, 38, 11, 1, 12, 12, 12, 12, 12, 12, 12, 1, 124, 124] 201
rigid atoms, others: [37, 12, 13, 14, 15, 16, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 366
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057677 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 200, 118, 118, 118, 52, 52, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 201, 201, 201, 201, 200, 118, 52, 12, 1, 1, 1, 1, 1, 1, 1, 12, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39])
total number of confs: 565
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057677 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057677
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057677/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057677
Building REAL300000057678
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057678'
/scratch/stefan/7769638/working/building/REAL300000057678 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057678

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057678/0 /scratch/stefan/7769638/working/building/REAL300000057678 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 709)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/709
`/scratch/stefan/7769638/working/3D/709' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C(C)OC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057678.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057678.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057678/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057678 none COC(=O)C(C)OC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 17, 38, 8, 17, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 25, 35, 35, 25, 29, 35, 35, 35, 35, 38, 38, 38, 17, 17, 17, 17, 1, 1, 1, 1, 5, 10, 25, 35, 35, 35, 35] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 260
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057678 none COC(=O)C(C)OC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 119, 201, 84, 119, 35, 35, 35, 17, 35, 35, 17, 17, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 201, 119, 119, 119, 119, 35, 35, 35, 35, 17, 10, 7, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 675
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057678 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057678
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057678/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057678
Building REAL300000057679
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057679'
/scratch/stefan/7769638/working/building/REAL300000057679 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057679

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057679/0 /scratch/stefan/7769638/working/building/REAL300000057679 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 710)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/710
`/scratch/stefan/7769638/working/3D/710' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)COC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057679.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057679.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057679/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057679 none COC(=O)COC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 29, 88, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 21, 27, 27, 24, 27, 27, 27, 27, 27, 88, 88, 88, 29, 29, 1, 1, 1, 1, 4, 10, 21, 27, 27, 27, 27] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 339
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057679 none COC(=O)COC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 169, 201, 71, 27, 27, 27, 13, 27, 27, 13, 13, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 201, 169, 169, 27, 27, 27, 27, 13, 8, 6, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 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, 38])
total number of confs: 707
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057679 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057679
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057679/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057679
Building REAL300000057680
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057680'
/scratch/stefan/7769638/working/building/REAL300000057680 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057680

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057680/0 /scratch/stefan/7769638/working/building/REAL300000057680 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 711)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/711
`/scratch/stefan/7769638/working/3D/711' -> `0.mol2'
Preparing input files

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

`REAL300000057680.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057680.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057680/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057680 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(F)C=NC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 8, 1, 1, 15, 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, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 33, 33, 33, 33, 33, 33, 33, 26, 26, 26, 14, 7, 1, 1, 1, 1, 33, 33] 33
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 33, 34, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 71
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057680 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(F)C=NC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 8, 1, 1, 15, 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, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 33, 33, 33, 33, 33, 1, 1] 33
rigid atoms, others: [1, 34, 33, 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])
total number of confs: 95
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057680 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057680
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057680/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057680
Building REAL300000057681
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057681'
/scratch/stefan/7769638/working/building/REAL300000057681 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057681

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057681/0 /scratch/stefan/7769638/working/building/REAL300000057681 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 712)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/712
`/scratch/stefan/7769638/working/3D/712' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1Cl)

`REAL300000057681.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057681/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057681 none COC1=CC=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
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, 10, 37, 44, 44, 37, 37, 44, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 37, 44, 44, 44, 44] 44
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 38, 39, 40, 41, 42, 43])
total number of confs: 154
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057681 none COC1=CC=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 44, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 13, 7, 1, 1, 1, 1] 44
rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 77
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057681 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057681
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057681/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057681
Building REAL300000057682
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057682'
/scratch/stefan/7769638/working/building/REAL300000057682 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057682

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057682/0 /scratch/stefan/7769638/working/building/REAL300000057682 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 713)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/713
`/scratch/stefan/7769638/working/3D/713' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC2(CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2)CO1)

`REAL300000057682.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057682.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057682/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057682 none CC1(C)CC2(CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 10, 10, 29, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 9, 29, 30, 30, 30, 30, 1, 1, 1, 1] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 41, 42, 7, 43, 40, 21, 22, 23, 33, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 89
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057682 none CC1(C)CC2(CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 13, 7, 1, 1, 1, 1, 30, 30, 30, 30] 30
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43])
total number of confs: 62
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057682 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057682
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057682/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057682
Building REAL300000057683
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057683'
/scratch/stefan/7769638/working/building/REAL300000057683 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057683

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057683/0 /scratch/stefan/7769638/working/building/REAL300000057683 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 714)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/714
`/scratch/stefan/7769638/working/3D/714' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC2(CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2)CO1)

`REAL300000057683.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057683/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057683 none CC1CC2(CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 31, 32, 32, 31, 32, 32, 32, 32, 32, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 31, 32, 32, 32, 32, 1, 1, 1, 1] 32
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 39, 40, 20, 21, 22, 26, 27, 28, 29, 30, 37] set([32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 31])
total number of confs: 94
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057683 none CC1CC2(CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 7, 1, 1, 1, 1, 32, 32, 32, 32] 32
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 67
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057683 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057683
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057683/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057683
Building REAL300000057684
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057684'
/scratch/stefan/7769638/working/building/REAL300000057684 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057684

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057684/0 /scratch/stefan/7769638/working/building/REAL300000057684 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 715)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/715
`/scratch/stefan/7769638/working/3D/715' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC=CC=C3C2)C=C1)

`REAL300000057684.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057684.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057684/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057684 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC=CC=C3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 10, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 23, 24, 25, 26] set([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])
total number of confs: 55
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057684 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC=CC=C3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 28
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 40, 23, 24, 25, 26, 27, 28])
total number of confs: 69
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057684 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057684
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057684/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057684
Building REAL300000057685
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057685'
/scratch/stefan/7769638/working/building/REAL300000057685 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057685

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057685/0 /scratch/stefan/7769638/working/building/REAL300000057685 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 716)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/716
`/scratch/stefan/7769638/working/3D/716' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1C1CCC1)

`REAL300000057685.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057685.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057685/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057685 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [32, 32, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 76, 76, 76, 76, 76, 109, 109, 109, 32, 32, 32, 14, 7, 1, 1, 1, 1, 76, 76, 109, 109, 109, 109, 109, 109, 109] 109
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057685 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 11, 11, 35, 35, 35, 72, 76, 76, 72, 72, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 35, 72, 76, 76, 76, 76, 1, 1, 7, 7, 7, 7, 7, 7, 7] 109
rigid atoms, others: [1, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057685 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [32, 7, 32, 32, 70, 70, 70, 109, 109, 109, 109, 109, 109, 109, 109, 109, 7, 7, 7, 7, 1, 1, 1, 1, 1, 32, 32, 32, 70, 109, 109, 109, 109, 109, 7, 7, 1, 1, 1, 1, 1, 1, 1] 109
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 306
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057685 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057685
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057685/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057685
Building REAL300000057686
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057686'
/scratch/stefan/7769638/working/building/REAL300000057686 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057686

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057686/0 /scratch/stefan/7769638/working/building/REAL300000057686 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 717)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/717
`/scratch/stefan/7769638/working/3D/717' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C2CCC2)N=C1)

`REAL300000057686.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057686/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057686 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [49, 49, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 141, 141, 141, 195, 195, 195, 141, 141, 49, 49, 49, 18, 7, 1, 1, 1, 1, 141, 195, 195, 195, 195, 195, 195, 195, 141] 195
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 418
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057686 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
195  conformations in input
total number of sets (complete confs): 195
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 13, 54, 54, 54, 123, 141, 141, 128, 128, 141, 141, 141, 141, 1, 1, 1, 1, 12, 12, 12, 1, 1, 13, 13, 13, 54, 123, 141, 141, 141, 141, 1, 12, 12, 12, 12, 12, 12, 12, 1] 195
rigid atoms, others: [1, 34, 42, 16, 17, 18, 19, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 490
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057686 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [85, 12, 85, 85, 142, 142, 142, 194, 195, 195, 195, 195, 195, 195, 195, 195, 12, 12, 1, 1, 1, 1, 1, 12, 12, 85, 85, 85, 142, 194, 195, 195, 195, 195, 12, 1, 1, 1, 1, 1, 1, 1, 12] 195
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42])
total number of confs: 531
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057686 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057686
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057686/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057686
Building REAL300000057687
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057687'
/scratch/stefan/7769638/working/building/REAL300000057687 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057687

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057687/0 /scratch/stefan/7769638/working/building/REAL300000057687 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 718)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/718
`/scratch/stefan/7769638/working/3D/718' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NCC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057687.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057687.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057687/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057687 none CC(C)(C)OC(=O)NCC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [99, 97, 99, 99, 72, 40, 72, 8, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 10, 15, 15, 13, 13, 15, 15, 15, 15, 1, 99, 99, 99, 99, 99, 99, 99, 99, 99, 40, 8, 8, 1, 1, 1, 1, 1, 3, 10, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [43, 8, 9, 10, 11, 12, 13, 14, 44, 40, 51, 52, 41, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50])
total number of confs: 336
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057687 none CC(C)(C)OC(=O)NCC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 201, 201, 201, 180, 137, 180, 50, 15, 15, 15, 15, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 15, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 50, 50, 15, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [49, 50, 47, 48, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52])
total number of confs: 620
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057687 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057687
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057687/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057687
Building REAL300000057688
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057688'
/scratch/stefan/7769638/working/building/REAL300000057688 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057688

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057688/0 /scratch/stefan/7769638/working/building/REAL300000057688 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 719)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/719
`/scratch/stefan/7769638/working/3D/719' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)C=C1)

`REAL300000057688.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057688/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057688 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 10, 10, 10, 20, 20, 50, 50, 20, 50, 50, 50, 126, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 9, 10, 20, 50, 50, 50, 50, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 424
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057688 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 43, 46, 46, 40, 19, 19, 19, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 29, 29, 46, 46, 46, 46, 40, 19, 11, 1, 1, 1, 1, 29, 29, 29, 29, 46, 46] 201
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43])
total number of confs: 173
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057688 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 197, 116, 116, 116, 77, 77, 29, 29, 29, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 197, 116, 77, 29, 29, 29, 29, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43])
total number of confs: 608
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057688 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057688
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057688/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057688
Building REAL300000057689
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057689'
/scratch/stefan/7769638/working/building/REAL300000057689 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057689

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057689/0 /scratch/stefan/7769638/working/building/REAL300000057689 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 720)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/720
`/scratch/stefan/7769638/working/3D/720' -> `0.mol2'
Preparing input files

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

`REAL300000057689.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057689.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057689/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057689 none COC(=O)C1(C2=CC=CC=C2)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.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', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [10, 10, 1, 10, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 1, 9, 10, 10, 30, 38, 38, 34, 34, 38, 38, 38, 38, 1, 10, 10, 10, 5, 5, 1, 5, 5, 1, 1, 9, 30, 38, 38, 38, 38, 1, 1] 80
rigid atoms, others: [2, 4, 5, 44, 11, 12, 13, 14, 45, 36, 27, 37] set([0, 1, 3, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 149
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057689 none COC(=O)C1(C2=CC=CC=C2)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.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', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [15, 15, 5, 15, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 20, 20, 20, 48, 53, 53, 52, 52, 53, 53, 53, 53, 5, 15, 15, 15, 1, 1, 1, 1, 1, 5, 5, 20, 48, 53, 53, 53, 53, 5, 5] 80
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 176
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057689 none COC(=O)C1(C2=CC=CC=C2)CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.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', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [77, 77, 38, 77, 38, 38, 53, 53, 38, 53, 53, 38, 38, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 77, 77, 77, 53, 53, 38, 53, 53, 38, 38, 13, 7, 1, 1, 1, 1, 38, 38] 80
rigid atoms, others: [40, 41, 42, 43, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45])
total number of confs: 266
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057689 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057689
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057689/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057689
Building REAL300000057690
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057690'
/scratch/stefan/7769638/working/building/REAL300000057690 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057690

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057690/0 /scratch/stefan/7769638/working/building/REAL300000057690 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 721)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/721
`/scratch/stefan/7769638/working/3D/721' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C(C=CS3)C2)C=C1)

`REAL300000057690.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057690.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057690/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057690 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C(C=CS3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 14, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 8, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 45
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057690 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C(C=CS3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 14, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 22
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 22, 23, 24, 25, 26, 27])
total number of confs: 59
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057690 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057690
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057690/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057690
Building REAL300000057691
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057691'
/scratch/stefan/7769638/working/building/REAL300000057691 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057691

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057691/0 /scratch/stefan/7769638/working/building/REAL300000057691 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 722)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/722
`/scratch/stefan/7769638/working/3D/722' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057691.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057691.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057691/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057691 none COC1=CC=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 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, 7, 7, 4, 7, 6, 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]
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, 1, 1, 1, 1, 1, 1, 1, 10, 10, 32, 32, 32, 71, 77, 77, 71, 73, 77, 77, 77, 77, 1, 3, 3, 3, 1, 1, 2, 2, 2, 10, 32, 71, 77, 77, 77, 77, 1] 78
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 39, 23, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 267
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057691 none COC1=CC=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 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, 7, 7, 4, 7, 6, 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]
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, 77, 77, 77, 77, 77, 77, 31, 31, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 78, 78, 78, 77, 77, 77, 77, 77, 31, 14, 7, 1, 1, 1, 1, 77] 78
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 126
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057691 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057691
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057691/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057691
Building REAL300000057692
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057692'
/scratch/stefan/7769638/working/building/REAL300000057692 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057692

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057692/0 /scratch/stefan/7769638/working/building/REAL300000057692 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 723)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/723
`/scratch/stefan/7769638/working/3D/723' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CN=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057692.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057692.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057692/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057692 none COC1=CN=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 8, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 35, 35, 35, 89, 91, 91, 89, 91, 91, 91, 91, 91, 3, 3, 3, 1, 1, 1, 10, 10, 10, 35, 89, 91, 91, 91, 91] 91
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 250
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057692 none COC1=CN=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 8, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 91, 39, 39, 39, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 91, 39, 39, 39, 14, 7, 1, 1, 1, 1] 91
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: 149
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057692 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057692
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057692/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057692
Building REAL300000057693
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057693'
/scratch/stefan/7769638/working/building/REAL300000057693 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057693

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057693/0 /scratch/stefan/7769638/working/building/REAL300000057693 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 724)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/724
`/scratch/stefan/7769638/working/3D/724' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=CN=C2C=C1)

`REAL300000057693.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057693.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057693/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057693 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=CN=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 64, 64, 64, 64, 64, 64, 64, 64, 64, 28, 28, 28, 16, 7, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64] 64
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 118
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057693 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=CN=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 37, 38, 38, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 37, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1] 64
rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 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])
total number of confs: 177
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057693 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057693
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057693/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057693
Building REAL300000057694
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057694'
/scratch/stefan/7769638/working/building/REAL300000057694 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057694

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057694/0 /scratch/stefan/7769638/working/building/REAL300000057694 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 725)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/725
`/scratch/stefan/7769638/working/3D/725' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC2=CC=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=C21)

`REAL300000057694.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057694.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057694/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057694 none CN1C=NC2=CC=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 1, 10, 10, 32, 32, 32, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 2, 2, 2, 1, 1, 1, 1, 10, 32, 63, 63, 63, 63, 63] 63
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 181
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057694 none CN1C=NC2=CC=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 63, 36, 36, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 63, 63, 63, 63, 63, 63, 63, 63, 36, 14, 7, 1, 1, 1, 1] 63
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 115
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057694 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057694
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057694/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057694
Building REAL300000057695
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057695'
/scratch/stefan/7769638/working/building/REAL300000057695 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057695

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057695/0 /scratch/stefan/7769638/working/building/REAL300000057695 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 726)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/726
`/scratch/stefan/7769638/working/3D/726' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(F)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057695.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057695/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057695 none CC1=CC(F)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 2, 2, 2, 1, 1, 6, 26, 49, 49, 49, 49, 49, 1] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 22, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 139
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057695 none CC1=CC(F)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 26, 14, 7, 1, 1, 1, 1, 49] 49
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057695 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057695
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057695/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057695
Building REAL300000057696
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057696'
/scratch/stefan/7769638/working/building/REAL300000057696 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057696

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057696/0 /scratch/stefan/7769638/working/building/REAL300000057696 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 727)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/727
`/scratch/stefan/7769638/working/3D/727' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057696.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057696.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057696/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057696 none CCC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.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.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']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 26, 26, 26, 46, 48, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 1, 1, 1, 1, 12, 26, 46, 48, 48, 48, 48] 77
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 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])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057696 none CCC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.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.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']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 48, 48, 48, 35, 48, 48, 29, 29, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 48, 46, 48, 48, 29, 14, 7, 1, 1, 1, 1] 77
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 312
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057696 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057696
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057696/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057696
Building REAL300000057697
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057697'
/scratch/stefan/7769638/working/building/REAL300000057697 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057697

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057697/0 /scratch/stefan/7769638/working/building/REAL300000057697 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 728)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/728
`/scratch/stefan/7769638/working/3D/728' -> `0.mol2'
Preparing input files

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

`REAL300000057697.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057697.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057697/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057697 none CN(C)C(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 8, 8, 28, 29, 29, 69, 74, 74, 72, 72, 74, 74, 74, 74, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 8, 28, 69, 74, 74, 74, 74, 1, 1] 83
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 41, 24, 25] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 225
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057697 none CN(C)C(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 83, 74, 83, 58, 74, 74, 34, 34, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 83, 83, 83, 83, 83, 83, 74, 74, 34, 12, 7, 1, 1, 1, 1, 74, 74] 83
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 226
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057697 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057697
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057697/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057697
Building REAL300000057698
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057698'
/scratch/stefan/7769638/working/building/REAL300000057698 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057698

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057698/0 /scratch/stefan/7769638/working/building/REAL300000057698 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 729)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/729
`/scratch/stefan/7769638/working/3D/729' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1C)

`REAL300000057698.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057698/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057698 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 21, 21, 21, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 21, 39, 39, 39, 39, 39, 2, 2, 2, 2, 2, 2] 39
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 121
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057698 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 39, 39, 29, 29, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 29, 16, 7, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39] 39
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 137
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057698 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057698
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057698/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057698
Building REAL300000057699
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057699'
/scratch/stefan/7769638/working/building/REAL300000057699 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057699

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057699/0 /scratch/stefan/7769638/working/building/REAL300000057699 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 730)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/730
`/scratch/stefan/7769638/working/3D/730' -> `0.mol2'
Preparing input files

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

`REAL300000057699.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057699/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057699 none CCN(CC)C(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 6, 4, 6, 7, 1, 4, 1, 1, 1, 1, 1, 6, 6, 10, 11, 11, 21, 23, 23, 21, 21, 23, 23, 23, 23, 1, 1, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 1, 1, 6, 10, 21, 23, 23, 23, 23, 1, 1] 57
rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 47, 48, 26, 27] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 123
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057699 none CCN(CC)C(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [49, 44, 35, 43, 48, 15, 35, 14, 23, 23, 8, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 23, 23, 49, 49, 49, 49, 49, 48, 48, 48, 48, 48, 23, 23, 8, 6, 6, 1, 1, 1, 1, 23, 23] 57
rigid atoms, others: [43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
total number of confs: 222
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057699 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057699
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057699/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057699
Building REAL300000057700
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057700'
/scratch/stefan/7769638/working/building/REAL300000057700 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057700

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057700/0 /scratch/stefan/7769638/working/building/REAL300000057700 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 731)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/731
`/scratch/stefan/7769638/working/3D/731' -> `0.mol2'
Preparing input files

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

`REAL300000057700.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057700/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057700 none CCNC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 5, 5, 5, 5, 5, 3, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 1] 23
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 41, 24, 25] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057700 none CCNC(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 13, 13, 13, 13, 9, 13, 13, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 23, 23, 23, 23, 23, 13, 13, 13, 5, 5, 3, 1, 1, 1, 1, 13, 13] 23
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 107
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057700 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057700
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057700/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057700
Building REAL300000057701
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057701'
/scratch/stefan/7769638/working/building/REAL300000057701 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057701

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057701/0 /scratch/stefan/7769638/working/building/REAL300000057701 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 732)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/732
`/scratch/stefan/7769638/working/3D/732' -> `0.mol2'
Preparing input files

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

`REAL300000057701.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057701.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057701/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057701 none CC(C)(C)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.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.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 34, 35, 35, 35, 35, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 16, 34, 35, 35, 35, 35] 35
rigid atoms, others: [1, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 37] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 95
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057701 none CC(C)(C)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.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.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 35, 35, 35, 26, 26, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 26, 13, 7, 1, 1, 1, 1] 35
rigid atoms, others: [41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 67
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057701 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057701
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057701/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057701
Building REAL300000057702
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057702'
/scratch/stefan/7769638/working/building/REAL300000057702 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057702

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057702/0 /scratch/stefan/7769638/working/building/REAL300000057702 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 733)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/733
`/scratch/stefan/7769638/working/3D/733' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C3CCCCCN23)C=C1)

`REAL300000057702.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057702.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057702/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057702 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C3CCCCCN23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 31, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 8, 14, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1] 49
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 95
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057702 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C3CCCCCN23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 51, 51, 49, 32, 31, 32, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 49, 31, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51] 51
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, 42, 41, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 137
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057702 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057702
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057702/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057702
Building REAL300000057703
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057703'
/scratch/stefan/7769638/working/building/REAL300000057703 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057703

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057703/0 /scratch/stefan/7769638/working/building/REAL300000057703 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 734)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/734
`/scratch/stefan/7769638/working/3D/734' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CN1)

`REAL300000057703.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057703/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057703 none CCOC(=O)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 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, 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: [25, 12, 10, 1, 10, 1, 1, 1, 3, 3, 7, 8, 8, 16, 21, 21, 19, 21, 21, 21, 21, 21, 1, 1, 1, 25, 25, 25, 25, 25, 3, 7, 16, 21, 21, 21, 21, 1, 1, 1] 47
rigid atoms, others: [3, 5, 6, 7, 39, 22, 23, 24, 38, 37] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057703 none CCOC(=O)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 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, 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, 45, 43, 21, 43, 21, 10, 10, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 21, 21, 47, 47, 47, 47, 47, 10, 6, 6, 1, 1, 1, 1, 21, 21, 21] 47
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39])
total number of confs: 129
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057703 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057703
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057703/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057703
Building REAL300000057704
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057704'
/scratch/stefan/7769638/working/building/REAL300000057704 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057704

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057704/0 /scratch/stefan/7769638/working/building/REAL300000057704 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 735)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/735
`/scratch/stefan/7769638/working/3D/735' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2SC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC2=C1)

`REAL300000057704.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057704.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057704/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057704 none COC1=CC=C2SC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 32, 33, 33, 77, 81, 81, 77, 79, 81, 81, 81, 81, 1, 1, 1, 3, 3, 3, 1, 1, 9, 32, 77, 81, 81, 81, 81, 1, 1] 81
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 39, 23, 24, 25, 38, 29, 30] set([0, 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: 242
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057704 none COC1=CC=C2SC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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
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, 44, 44, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81, 44, 14, 7, 1, 1, 1, 1, 81, 81] 81
rigid atoms, others: [34, 35, 36, 37, 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, 38, 39])
total number of confs: 132
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057704 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057704
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057704/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057704
Building REAL300000057705
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057705'
/scratch/stefan/7769638/working/building/REAL300000057705 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057705

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057705/0 /scratch/stefan/7769638/working/building/REAL300000057705 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 736)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/736
`/scratch/stefan/7769638/working/3D/736' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CON=C2C2CC2)C=C1)

`REAL300000057705.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057705.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057705/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057705 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CON=C2C2CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 12, 8, 1, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 16, 16, 16, 52, 52, 100, 100, 100, 100, 100, 136, 136, 1, 1, 1, 1, 8, 16, 52, 100, 136, 136, 136, 136, 136, 1, 1] 136
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 307
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057705 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CON=C2C2CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 12, 8, 1, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [86, 82, 86, 78, 86, 86, 78, 34, 34, 34, 12, 12, 1, 1, 1, 1, 1, 1, 1, 9, 9, 86, 86, 86, 86, 78, 34, 12, 1, 9, 9, 9, 9, 9, 86, 86] 118
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 291
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057705 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CON=C2C2CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 12, 8, 1, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 118, 118, 118, 118, 72, 72, 72, 37, 37, 9, 9, 8, 9, 9, 1, 1, 1, 1, 118, 118, 118, 118, 118, 72, 37, 9, 1, 1, 1, 1, 1, 118, 118] 118
rigid atoms, others: [32, 33, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35])
total number of confs: 329
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057705 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057705
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057705/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057705
Building REAL300000057706
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057706'
/scratch/stefan/7769638/working/building/REAL300000057706 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057706

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057706/0 /scratch/stefan/7769638/working/building/REAL300000057706 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 737)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/737
`/scratch/stefan/7769638/working/3D/737' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC=C(Cl)C(Cl)=C32)C=C1)

`REAL300000057706.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057706/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057706 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC=C(Cl)C(Cl)=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 8, 14, 16, 16, 16, 1, 1] 16
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057706 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC=C(Cl)C(Cl)=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 5, 1, 1, 1, 16, 16] 16
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33, 24, 25, 26, 27, 28, 29])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057706 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057706
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057706/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057706
Building REAL300000057707
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057707'
/scratch/stefan/7769638/working/building/REAL300000057707 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057707

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057707/0 /scratch/stefan/7769638/working/building/REAL300000057707 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 738)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/738
`/scratch/stefan/7769638/working/3D/738' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057707.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057707/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057707 none CCN1N=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 34, 34, 34, 78, 84, 84, 78, 82, 84, 84, 84, 84, 6, 6, 6, 6, 6, 1, 1, 12, 12, 12, 34, 78, 84, 84, 84, 84] 86
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 279
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057707 none CCN1N=CC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [86, 84, 84, 84, 84, 84, 39, 39, 39, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 86, 86, 86, 86, 86, 84, 84, 39, 39, 39, 16, 7, 1, 1, 1, 1] 86
rigid atoms, others: [35, 36, 37, 38, 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])
total number of confs: 150
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057707 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057707
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057707/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057707
Building REAL300000057708
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057708'
/scratch/stefan/7769638/working/building/REAL300000057708 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057708

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057708/0 /scratch/stefan/7769638/working/building/REAL300000057708 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 739)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/739
`/scratch/stefan/7769638/working/3D/739' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(Cl)=C2)C=C1)

`REAL300000057708.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057708/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057708 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 10, 10, 10, 26, 26, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 6, 10, 26, 45, 45, 45, 1, 1] 45
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057708 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 19, 18, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 18, 6, 1, 1, 1, 46, 46] 46
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, 31])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057708 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057708
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057708/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057708
Building REAL300000057709
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057709'
/scratch/stefan/7769638/working/building/REAL300000057709 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057709

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057709/0 /scratch/stefan/7769638/working/building/REAL300000057709 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 740)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/740
`/scratch/stefan/7769638/working/3D/740' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(C3=CC=CC=C3)=NO2)C=C1)

`REAL300000057709.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057709/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057709 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(C3=CC=CC=C3)=NO2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 3, 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, 4, 5, 5, 5, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 4, 5, 7, 9, 9, 9, 9, 9, 9, 1, 1] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 37] set([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: 21
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057709 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(C3=CC=CC=C3)=NO2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [77, 75, 77, 75, 77, 77, 71, 29, 29, 29, 8, 8, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 77, 77, 77, 77, 71, 28, 8, 1, 7, 7, 2, 7, 7, 77, 77] 81
rigid atoms, others: [12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 236
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057709 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(C3=CC=CC=C3)=NO2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 81, 81, 81, 81, 80, 51, 51, 51, 25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 81, 81, 81, 81, 80, 51, 25, 7, 1, 1, 1, 1, 1, 81, 81] 81
rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38])
total number of confs: 230
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057709 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057709
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057709/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057709
Building REAL300000057710
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057710'
/scratch/stefan/7769638/working/building/REAL300000057710 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057710

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057710/0 /scratch/stefan/7769638/working/building/REAL300000057710 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 741)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/741
`/scratch/stefan/7769638/working/3D/741' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C1=CC=CC=C1)

`REAL300000057710.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057710.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057710/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057710 none NC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 8, 8, 31, 31, 31, 66, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 5, 5, 3, 5, 5, 1, 1, 8, 30, 66, 67, 67, 67, 67, 1, 5, 5, 3, 5, 5] 116
rigid atoms, others: [0, 1, 2, 3, 36, 18, 19, 20, 21, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 189
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057710 none NC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 43, 43, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 67, 67, 67, 67, 116, 116, 116, 116, 116, 67, 67, 43, 16, 7, 1, 1, 1, 1, 67, 116, 116, 116, 116, 116] 116
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 224
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057710 none NC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 29, 29, 71, 71, 71, 114, 116, 116, 116, 116, 116, 116, 116, 116, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 71, 114, 116, 116, 116, 116, 5, 1, 1, 1, 1, 1] 116
rigid atoms, others: [37, 38, 39, 40, 41, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 316
number of broken/clashed sets: 62
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057710 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057710
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057710/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057710
Building REAL300000057711
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057711'
/scratch/stefan/7769638/working/building/REAL300000057711 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057711

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057711/0 /scratch/stefan/7769638/working/building/REAL300000057711 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 742)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/742
`/scratch/stefan/7769638/working/3D/742' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000057711.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057711.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057711/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057711 none CCC(=O)NC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 51, 51, 51, 92, 119, 119, 92, 107, 119, 119, 119, 119, 1, 1, 34, 34, 34, 34, 34, 5, 1, 1, 13, 13, 13, 51, 92, 119, 119, 119, 119, 1, 1] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 44, 45, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 564
number of broken/clashed sets: 157
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057711 none CCC(=O)NC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 175, 168, 168, 76, 33, 119, 119, 33, 33, 33, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 201, 201, 201, 201, 201, 168, 119, 119, 33, 33, 33, 10, 6, 1, 1, 1, 1, 119, 119] 201
rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45])
total number of confs: 818
number of broken/clashed sets: 157
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057711 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057711
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057711/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057711
Building REAL300000057712
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057712'
/scratch/stefan/7769638/working/building/REAL300000057712 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057712

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057712/0 /scratch/stefan/7769638/working/building/REAL300000057712 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 743)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/743
`/scratch/stefan/7769638/working/3D/743' -> `0.mol2'
Preparing input files

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

`REAL300000057712.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057712.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057712/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057712 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC=CC(C)=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 5, 1, 14, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [28, 28, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 28, 28, 28, 14, 7, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49] 49
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 98
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057712 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC=CC(C)=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 5, 1, 14, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 31, 31, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 31, 49, 49, 49, 49, 49, 2, 2, 2, 1, 1, 1, 2, 2, 2] 49
rigid atoms, others: [1, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 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, 42, 43, 44])
total number of confs: 147
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057712 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057712
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057712/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057712
Building REAL300000057713
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057713'
/scratch/stefan/7769638/working/building/REAL300000057713 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057713

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057713/0 /scratch/stefan/7769638/working/building/REAL300000057713 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 744)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/744
`/scratch/stefan/7769638/working/3D/744' -> `0.mol2'
Preparing input files

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

`REAL300000057713.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057713.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057713/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057713 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC(C)=CC(C)=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 5, 1, 14, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 32, 32, 32, 16, 7, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51] 51
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 96
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057713 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC(C)=CC(C)=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 5, 1, 14, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 34, 34, 34, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 33, 51, 51, 51, 51, 51, 2, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2] 51
rigid atoms, others: [1, 40, 44, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 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, 39, 41, 42, 43, 45, 46, 47])
total number of confs: 166
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057713 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057713
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057713/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057713
Building REAL300000057714
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057714'
/scratch/stefan/7769638/working/building/REAL300000057714 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057714

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057714/0 /scratch/stefan/7769638/working/building/REAL300000057714 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 745)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/745
`/scratch/stefan/7769638/working/3D/745' -> `0.mol2'
Preparing input files

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

`REAL300000057714.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057714.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057714/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057714 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C(C)(C)C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 5, 5, 5, 5, 8, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 43, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 13, 7, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 43
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 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: 81
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057714 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C(C)(C)C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 5, 5, 5, 5, 8, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [8, 1, 8, 8, 21, 22, 22, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 4, 4, 4, 1, 9, 9, 9, 21, 43, 43, 43, 43, 43, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 43
rigid atoms, others: [1, 34, 16, 17, 18, 19, 20, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 139
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057714 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057714
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057714/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057714
Building REAL300000057715
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057715'
/scratch/stefan/7769638/working/building/REAL300000057715 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057715

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057715/0 /scratch/stefan/7769638/working/building/REAL300000057715 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 746)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/746
`/scratch/stefan/7769638/working/3D/746' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC2(F)F)C=C1)

`REAL300000057715.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057715.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057715/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057715 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC2(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 8, 15, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 20, 21, 22, 23] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057715 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCC2(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 17
rigid atoms, others: [32, 33, 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, 8, 9, 34, 35, 20, 21, 22, 23, 24, 25])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057715 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057715
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057715/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057715
Building REAL300000057716
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057716'
/scratch/stefan/7769638/working/building/REAL300000057716 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057716

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057716/0 /scratch/stefan/7769638/working/building/REAL300000057716 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 747)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/747
`/scratch/stefan/7769638/working/3D/747' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCC1=CC=C(O)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057716.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057716.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057716/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057716 none N#CCC1=CC=C(O)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 4, 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
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 41, 47, 47, 41, 45, 47, 47, 47, 47, 1, 7, 7, 1, 1, 2, 7, 21, 41, 47, 47, 47, 47, 1] 150
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 24, 27, 28, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 179
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057716 none N#CCC1=CC=C(O)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 4, 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
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 47, 47, 33, 47, 47, 47, 30, 30, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 47, 75, 75, 47, 47, 94, 30, 13, 7, 1, 1, 1, 1, 47] 150
rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37])
total number of confs: 376
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057716 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057716
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057716/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057716
Building REAL300000057717
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057717'
/scratch/stefan/7769638/working/building/REAL300000057717 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057717

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057717/0 /scratch/stefan/7769638/working/building/REAL300000057717 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 748)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/748
`/scratch/stefan/7769638/working/3D/748' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C1CC1)

`REAL300000057717.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057717/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057717 none NC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C1CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 6, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 10, 10, 34, 35, 35, 84, 91, 91, 89, 91, 91, 91, 91, 91, 1, 1, 1, 1, 7, 7, 1, 1, 10, 34, 84, 91, 91, 91, 91, 1, 7, 7, 7, 7, 7] 120
rigid atoms, others: [0, 1, 2, 3, 33, 18, 19, 20, 21, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 253
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057717 none NC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C1CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 6, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 6, 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]
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: [91, 91, 56, 56, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 91, 91, 91, 91, 120, 120, 91, 91, 56, 16, 7, 1, 1, 1, 1, 91, 120, 120, 120, 120, 120] 120
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 276
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057717 none NC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C1CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 6, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 6, 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]
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: [7, 7, 7, 7, 35, 35, 73, 73, 73, 119, 120, 120, 120, 120, 120, 120, 120, 120, 7, 7, 1, 1, 1, 1, 7, 7, 35, 73, 119, 120, 120, 120, 120, 7, 1, 1, 1, 1, 1] 120
rigid atoms, others: [34, 35, 36, 37, 38, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 340
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057717 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057717
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057717/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057717
Building REAL300000057718
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057718'
/scratch/stefan/7769638/working/building/REAL300000057718 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057718

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057718/0 /scratch/stefan/7769638/working/building/REAL300000057718 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 749)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/749
`/scratch/stefan/7769638/working/3D/749' -> `0.mol2'
Preparing input files

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

`REAL300000057718.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057718.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057718/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057718 none CCN(C)C(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [21, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 6, 6, 12, 13, 13, 29, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 21, 21, 21, 21, 21, 13, 13, 13, 1, 1, 6, 12, 29, 33, 33, 33, 33, 1, 1] 99
rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 44, 45, 25, 36, 26] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 179
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057718 none CCN(C)C(=O)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 65, 50, 65, 19, 50, 11, 33, 33, 11, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 99, 99, 99, 99, 99, 65, 65, 65, 33, 33, 11, 5, 5, 1, 1, 1, 1, 33, 33] 99
rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45])
total number of confs: 455
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057718 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057718
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057718/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057718
Building REAL300000057719
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057719'
/scratch/stefan/7769638/working/building/REAL300000057719 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057719

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057719/0 /scratch/stefan/7769638/working/building/REAL300000057719 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 750)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/750
`/scratch/stefan/7769638/working/3D/750' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1CCC2=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC=C21)

`REAL300000057719.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057719/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057719 none CCN1CCC2=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 26, 26, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 6, 25, 56, 56, 56, 56, 56, 1, 1] 56
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 44, 34, 43, 35, 23, 24, 25, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 36, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057719 none CCN1CCC2=CC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 28, 28, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 28, 12, 7, 1, 1, 1, 1, 56, 56] 56
rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44])
total number of confs: 106
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057719 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057719
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057719/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057719
Building REAL300000057720
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057720'
/scratch/stefan/7769638/working/building/REAL300000057720 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057720

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057720/0 /scratch/stefan/7769638/working/building/REAL300000057720 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 751)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/751
`/scratch/stefan/7769638/working/3D/751' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CN=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1)

`REAL300000057720.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057720.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057720/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057720 none COC(=O)C1=CN=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.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']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 30, 30, 26, 26, 30, 30, 30, 30, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 26, 30, 30, 30, 30, 1] 52
rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 13, 44, 36, 26, 27, 37, 31] set([0, 1, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 38, 39, 40, 41, 42, 43])
total number of confs: 112
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057720 none COC(=O)C1=CN=C2CCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.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']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 30, 52, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 30, 52, 52, 52, 30, 30, 30, 30, 30, 30, 30, 10, 7, 1, 1, 1, 1, 30] 52
rigid atoms, others: [40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 145
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057720 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057720
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057720/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057720
Building REAL300000057721
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057721'
/scratch/stefan/7769638/working/building/REAL300000057721 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057721

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057721/0 /scratch/stefan/7769638/working/building/REAL300000057721 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 752)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/752
`/scratch/stefan/7769638/working/3D/752' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC2(CO1)CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CC2)

`REAL300000057721.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057721.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057721/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057721 none CC1(C)CC2(CO1)CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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
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, 1, 1, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 31, 31, 1, 1, 1, 1] 31
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45])
total number of confs: 91
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057721 none CC1(C)CC2(CO1)CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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
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, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 7, 1, 1, 1, 1, 31, 31, 31, 31] 31
rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49])
total number of confs: 60
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057721 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057721
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057721/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057721
Building REAL300000057722
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057722'
/scratch/stefan/7769638/working/building/REAL300000057722 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057722

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057722/0 /scratch/stefan/7769638/working/building/REAL300000057722 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 753)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/753
`/scratch/stefan/7769638/working/3D/753' -> `0.mol2'
Preparing input files

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

`REAL300000057722.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057722.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057722/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057722 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Cl)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 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]
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: [22, 22, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 45, 45, 45, 45, 45, 45, 45, 45, 22, 22, 22, 14, 7, 1, 1, 1, 1, 45, 45, 45, 45, 45, 90] 90
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 175
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057722 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Cl)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 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]
1  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 23, 45, 45, 45, 45, 45, 1, 2, 2, 2, 1, 2] 90
rigid atoms, others: [1, 34, 38, 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, 35, 36, 37, 39])
total number of confs: 123
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057722 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057722/1 /scratch/stefan/7769638/working/building/REAL300000057722 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 754)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/754
`/scratch/stefan/7769638/working/3D/754' -> `1.mol2'
Preparing input files

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

`REAL300000057722.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057722.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057722/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057722 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Cl)=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 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, 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]
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: [36, 36, 20, 20, 7, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 41, 41, 41, 41, 41, 41, 41, 41, 36, 36, 36, 20, 7, 1, 1, 1, 1, 41, 41, 41, 41, 41] 41
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 85
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057722 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Cl)=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 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, 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]
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: [5, 1, 5, 5, 13, 13, 13, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 41, 41, 41, 41, 41, 1, 2, 2, 2, 1] 41
rigid atoms, others: [1, 34, 38, 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, 35, 36, 37])
total number of confs: 109
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057722 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057722
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057722/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057722/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057722
Building REAL300000057723
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057723'
/scratch/stefan/7769638/working/building/REAL300000057723 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057723

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057723/0 /scratch/stefan/7769638/working/building/REAL300000057723 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 755)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/755
`/scratch/stefan/7769638/working/3D/755' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C(C)C)

`REAL300000057723.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057723.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057723/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057723 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 10, 10, 25, 25, 25, 57, 59, 59, 57, 58, 59, 59, 59, 59, 1, 1, 1, 1, 3, 3, 2, 2, 2, 10, 25, 57, 59, 59, 59, 59, 1, 3, 4, 4, 4, 3, 3, 3] 59
rigid atoms, others: [0, 1, 2, 3, 34, 18, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 196
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057723 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 39, 39, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 39, 14, 7, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59] 59
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057723 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057723
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057723/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057723
Building REAL300000057724
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057724'
/scratch/stefan/7769638/working/building/REAL300000057724 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057724

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057724/0 /scratch/stefan/7769638/working/building/REAL300000057724 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 756)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/756
`/scratch/stefan/7769638/working/3D/756' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Cl)=C2OCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1)

`REAL300000057724.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057724.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057724/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057724 none CC1=CC(Cl)=C2OCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 16, 1, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 8, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 19, 19, 19, 19, 19, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 32, 24, 25, 33, 29, 30, 31] set([34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28])
total number of confs: 55
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057724 none CC1=CC(Cl)=C2OCCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 16, 1, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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]
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, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 7, 1, 1, 1, 1, 19] 19
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 43
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057724 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057724
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057724/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057724
Building REAL300000057725
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057725'
/scratch/stefan/7769638/working/building/REAL300000057725 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057725

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057725/0 /scratch/stefan/7769638/working/building/REAL300000057725 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 757)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/757
`/scratch/stefan/7769638/working/3D/757' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl)

`REAL300000057725.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057725.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057725/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057725 none CSC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 14, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 8, 8, 30, 31, 31, 75, 87, 87, 75, 75, 87, 87, 87, 87, 1, 1, 1, 8, 8, 8, 1, 1, 8, 30, 75, 87, 87, 87, 87, 1] 111
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 36, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057725 none CSC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 14, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [111, 87, 75, 87, 87, 46, 46, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 87, 87, 87, 111, 111, 111, 87, 87, 46, 16, 7, 1, 1, 1, 1, 87] 111
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 258
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057725 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057725
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057725/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057725
Building REAL300000057726
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057726'
/scratch/stefan/7769638/working/building/REAL300000057726 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057726

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057726/0 /scratch/stefan/7769638/working/building/REAL300000057726 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 758)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/758
`/scratch/stefan/7769638/working/3D/758' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1C1CC1)

`REAL300000057726.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057726.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057726/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057726 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 23, 24, 24, 57, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 5, 5, 2, 2, 2, 1, 6, 23, 57, 58, 58, 58, 58, 1, 1, 5, 5, 5, 5, 5] 86
rigid atoms, others: [0, 1, 2, 3, 4, 37, 19, 20, 21, 22, 36, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42])
total number of confs: 171
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057726 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 58, 30, 30, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 58, 58, 30, 30, 86, 86, 58, 58, 58, 58, 30, 11, 7, 1, 1, 1, 1, 58, 58, 86, 86, 86, 86, 86] 86
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 346
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057726 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 2, 2, 14, 18, 43, 43, 43, 86, 86, 86, 86, 86, 86, 86, 86, 86, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 14, 43, 86, 86, 86, 86, 86, 5, 5, 1, 1, 1, 1, 1] 86
rigid atoms, others: [38, 39, 40, 41, 42, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 243
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057726 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057726
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057726/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057726
Building REAL300000057727
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057727'
/scratch/stefan/7769638/working/building/REAL300000057727 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057727

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057727/0 /scratch/stefan/7769638/working/building/REAL300000057727 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 759)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/759
`/scratch/stefan/7769638/working/3D/759' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC2=C1CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C2)

`REAL300000057727.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057727.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057727/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057727 none COC1=CC=CC2=C1CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 1, 1] 16
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46] set([0, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 39, 40, 41, 42, 43, 44])
total number of confs: 49
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057727 none COC1=CC=CC2=C1CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 16, 16, 16, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 5, 1, 1, 1, 1, 16, 16] 16
rigid atoms, others: [41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46])
total number of confs: 35
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057727 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057727
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057727/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057727
Building REAL300000057728
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057728'
/scratch/stefan/7769638/working/building/REAL300000057728 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057728

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057728/0 /scratch/stefan/7769638/working/building/REAL300000057728 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 760)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/760
`/scratch/stefan/7769638/working/3D/760' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=N1)

`REAL300000057728.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057728.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057728/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057728 none CCOC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=N1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 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, 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
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [17, 5, 1, 1, 1, 1, 1, 8, 8, 28, 29, 29, 67, 72, 72, 71, 71, 72, 72, 72, 72, 1, 1, 1, 18, 18, 18, 17, 17, 1, 8, 28, 67, 72, 72, 72, 72, 1, 1] 86
rigid atoms, others: [2, 3, 4, 5, 6, 21, 22, 23, 38, 29, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 261
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057728 none CCOC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=N1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 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, 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
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [86, 86, 72, 72, 72, 36, 36, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 72, 72, 72, 86, 86, 86, 86, 86, 72, 36, 15, 7, 1, 1, 1, 1, 72, 72] 86
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 149
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057728 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057728
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057728/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057728
Building REAL300000057729
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057729'
/scratch/stefan/7769638/working/building/REAL300000057729 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057729

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057729/0 /scratch/stefan/7769638/working/building/REAL300000057729 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 761)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/761
`/scratch/stefan/7769638/working/3D/761' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl)

`REAL300000057729.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057729.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057729/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057729 none CC1=NN(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 9, 9, 9, 9, 9, 1, 1, 1] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 40, 32, 23, 24, 25, 26, 27, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057729 none CC1=NN(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 9, 9, 9, 9, 9, 1, 1, 1] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 40, 32, 23, 24, 25, 26, 27, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 29
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057729 none CC1=NN(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 3, 1, 1, 1, 1, 9, 9, 9] 9
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, 42])
total number of confs: 27
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057729 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057729
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057729/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057729
Building REAL300000057730
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057730'
/scratch/stefan/7769638/working/building/REAL300000057730 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057730

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057730/0 /scratch/stefan/7769638/working/building/REAL300000057730 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 762)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/762
`/scratch/stefan/7769638/working/3D/762' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C1CC1)

`REAL300000057730.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057730.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057730/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057730 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C1CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 32, 33, 33, 66, 69, 69, 68, 69, 69, 69, 69, 69, 1, 1, 1, 5, 5, 2, 2, 2, 1, 1, 11, 32, 66, 69, 69, 69, 69, 1, 5, 5, 5, 5, 5] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 28, 29, 37] 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, 38, 39, 40, 41, 42])
total number of confs: 200
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057730 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C1CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [69, 63, 69, 69, 34, 34, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 69, 69, 69, 96, 96, 69, 69, 69, 69, 69, 34, 17, 7, 1, 1, 1, 1, 69, 96, 96, 96, 96, 96] 96
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 272
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057730 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1C1CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [5, 5, 5, 5, 5, 5, 23, 23, 52, 52, 52, 94, 96, 96, 96, 96, 96, 96, 96, 96, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 23, 52, 94, 96, 96, 96, 96, 5, 1, 1, 1, 1, 1] 96
rigid atoms, others: [38, 39, 40, 41, 42, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 260
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057730 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057730
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057730/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057730
Building REAL300000057731
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057731'
/scratch/stefan/7769638/working/building/REAL300000057731 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057731

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057731/0 /scratch/stefan/7769638/working/building/REAL300000057731 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 763)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/763
`/scratch/stefan/7769638/working/3D/763' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C(C)=C2)C=C1)

`REAL300000057731.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057731.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057731/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057731 none CC1=NN(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C(C)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 7, 7, 2, 2, 18, 20, 38, 38, 38, 59, 59, 59, 59, 59, 59, 59, 59, 59, 7, 7, 7, 1, 1, 2, 2, 2, 7, 7, 18, 38, 59, 59, 59, 59, 59, 7, 7, 7, 7, 1, 1] 59
rigid atoms, others: [0, 1, 2, 3, 4, 44, 45, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057731 none CC1=NN(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C(C)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 7, 7, 1, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 11, 25, 45, 45, 45, 45, 45, 2, 2, 2, 1, 7, 7] 59
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 43, 23, 24, 25, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057731 none CC1=NN(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C(C)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 29, 29, 45, 45, 29, 29, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 59, 59, 59, 59, 59, 45, 45, 29, 12, 7, 1, 1, 1, 1, 45, 45, 45, 45, 59, 59] 59
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45])
total number of confs: 141
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057731 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057731
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057731/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057731
Building REAL300000057732
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057732'
/scratch/stefan/7769638/working/building/REAL300000057732 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057732

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057732/0 /scratch/stefan/7769638/working/building/REAL300000057732 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 764)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/764
`/scratch/stefan/7769638/working/3D/764' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057732.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057732.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057732/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057732 none CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 8, 1, 1, 16, 1, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 12, 28, 28, 28, 50, 54, 54, 53, 54, 54, 54, 54, 54, 2, 2, 2, 1, 5, 5, 1, 1, 12, 28, 50, 54, 54, 54, 54] 70
rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 34, 13, 35, 31] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 160
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057732 none CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 8, 1, 1, 16, 1, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 2, 21, 22, 42, 42, 42, 68, 70, 70, 70, 70, 70, 70, 70, 70, 5, 5, 5, 5, 1, 1, 5, 5, 21, 42, 68, 70, 70, 70, 70] 70
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057732 none CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 8, 1, 1, 16, 1, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [54, 54, 54, 39, 42, 70, 70, 70, 70, 70, 54, 54, 31, 31, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 54, 54, 54, 54, 70, 70, 54, 54, 31, 14, 7, 1, 1, 1, 1] 70
rigid atoms, others: [39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 179
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057732 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057732
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057732/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057732
Building REAL300000057733
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057733'
/scratch/stefan/7769638/working/building/REAL300000057733 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057733

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057733/0 /scratch/stefan/7769638/working/building/REAL300000057733 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 765)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/765
`/scratch/stefan/7769638/working/3D/765' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057733.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057733.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057733/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057733 none CNC(=O)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 14, 15, 15, 14, 14, 15, 15, 15, 15, 9, 9, 9, 9, 1, 1, 1, 1, 5, 7, 14, 15, 15, 15, 15] 20
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 3, 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])
total number of confs: 70
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057733 none CNC(=O)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 15, 20, 15, 15, 15, 15, 15, 8, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 15, 15, 15, 15, 8, 6, 6, 1, 1, 1, 1] 20
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])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057733 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057733
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057733/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057733
Building REAL300000057734
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057734'
/scratch/stefan/7769638/working/building/REAL300000057734 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057734

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057734/0 /scratch/stefan/7769638/working/building/REAL300000057734 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 766)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/766
`/scratch/stefan/7769638/working/3D/766' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCNC(=O)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057734.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057734.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057734/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057734 none CCNC(=O)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 20, 25, 25, 20, 20, 25, 25, 25, 25, 22, 22, 22, 22, 22, 9, 1, 1, 1, 1, 6, 11, 20, 25, 25, 25, 25] 39
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 35] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 175
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057734 none CCNC(=O)C1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 34, 34, 25, 34, 25, 25, 25, 25, 25, 12, 12, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 34, 25, 25, 25, 25, 12, 6, 6, 1, 1, 1, 1] 39
rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 109
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057734 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057734
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057734/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057734
Building REAL300000057735
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057735'
/scratch/stefan/7769638/working/building/REAL300000057735 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057735

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057735/0 /scratch/stefan/7769638/working/building/REAL300000057735 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 767)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/767
`/scratch/stefan/7769638/working/3D/767' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)C=C1)

`REAL300000057735.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057735.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057735/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057735 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 3, 5, 5, 9, 9, 9, 9, 17, 17, 17, 17, 1, 1] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057735 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [66, 62, 66, 62, 66, 66, 62, 27, 27, 27, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 66, 66, 66, 66, 62, 27, 12, 1, 1, 1, 1, 7, 7, 2, 7, 66, 66] 103
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057735 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [103, 103, 103, 103, 103, 103, 103, 50, 50, 50, 26, 26, 7, 7, 7, 5, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 50, 26, 7, 7, 7, 7, 1, 1, 1, 1, 103, 103] 103
rigid atoms, others: [37, 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, 41, 42])
total number of confs: 287
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057735 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057735
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057735/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057735
Building REAL300000057736
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057736'
/scratch/stefan/7769638/working/building/REAL300000057736 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057736

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057736/0 /scratch/stefan/7769638/working/building/REAL300000057736 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 768)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/768
`/scratch/stefan/7769638/working/3D/768' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(Br)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057736.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057736.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057736/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057736 none CCC1=CC(Br)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 30, 31, 31, 74, 77, 77, 74, 76, 77, 77, 77, 77, 1, 8, 8, 8, 8, 8, 1, 12, 30, 74, 77, 77, 77, 77] 123
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057736 none CCC1=CC(Br)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [123, 77, 77, 77, 77, 77, 42, 42, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 77, 123, 123, 123, 123, 123, 77, 42, 16, 7, 1, 1, 1, 1] 123
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 407
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057736 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057736
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057736/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057736
Building REAL300000057737
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057737'
/scratch/stefan/7769638/working/building/REAL300000057737 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057737

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057737/0 /scratch/stefan/7769638/working/building/REAL300000057737 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 769)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/769
`/scratch/stefan/7769638/working/3D/769' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057737.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057737.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057737/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057737 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3] 5
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])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057737 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1] 5
rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 23
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057737 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057737
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057737/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057737
Building REAL300000057738
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057738'
/scratch/stefan/7769638/working/building/REAL300000057738 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057738

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057738/0 /scratch/stefan/7769638/working/building/REAL300000057738 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 770)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/770
`/scratch/stefan/7769638/working/3D/770' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC2=C(C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)O2)N1)

`REAL300000057738.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057738/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057738 none COC(=O)C1=CC2=C(C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)O2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 3, 3, 3, 1, 1, 6, 14, 37, 37, 37, 37, 37, 1] 63
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 39, 25, 26, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057738 none COC(=O)C1=CC2=C(C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)O2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 37, 63, 37, 37, 37, 37, 37, 24, 24, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 63, 63, 63, 37, 37, 24, 8, 5, 1, 1, 1, 1, 37] 63
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])
total number of confs: 178
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057738 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057738/1 /scratch/stefan/7769638/working/building/REAL300000057738 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 771)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/771
`/scratch/stefan/7769638/working/3D/771' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC2=C(C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)O2)[N-]1)

`REAL300000057738.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057738/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057738 none COC(=O)C1=CC2=C(C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)O2)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 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
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 17, 17, 53, 55, 55, 54, 55, 55, 55, 55, 55, 1, 1, 7, 7, 7, 1, 1, 6, 16, 53, 55, 55, 55, 55] 72
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 25, 26, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057738 none COC(=O)C1=CC2=C(C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)O2)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 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
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 55, 72, 55, 55, 55, 55, 55, 30, 30, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 55, 55, 72, 72, 72, 55, 55, 30, 12, 7, 1, 1, 1, 1] 72
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])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057738 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057738
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057738/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057738/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057738
Building REAL300000057739
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057739'
/scratch/stefan/7769638/working/building/REAL300000057739 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057739

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057739/0 /scratch/stefan/7769638/working/building/REAL300000057739 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 772)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/772
`/scratch/stefan/7769638/working/3D/772' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057739.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057739/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057739 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 6, 6, 16, 17, 17, 37, 39, 39, 38, 39, 39, 39, 39, 39, 1, 4, 4, 4, 1, 1, 6, 16, 37, 39, 39, 39, 39] 41
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057739 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 39, 39, 39, 39, 30, 30, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 39, 41, 41, 41, 39, 39, 30, 10, 7, 1, 1, 1, 1] 41
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 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
/scratch/stefan/7769638/working/building/REAL300000057739 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057739
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057739/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057739
Building REAL300000057740
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057740'
/scratch/stefan/7769638/working/building/REAL300000057740 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057740

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057740/0 /scratch/stefan/7769638/working/building/REAL300000057740 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 773)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/773
`/scratch/stefan/7769638/working/3D/773' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057740.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057740.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057740/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057740 none COCCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 48, 30, 9, 1, 1, 1, 1, 1, 1, 6, 6, 20, 21, 21, 43, 52, 52, 47, 52, 52, 52, 52, 52, 1, 71, 71, 71, 48, 48, 30, 30, 1, 1, 6, 20, 43, 52, 52, 52, 52] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 379
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057740 none COCCOC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 148, 76, 52, 52, 52, 52, 23, 23, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 52, 201, 201, 201, 201, 201, 148, 148, 52, 52, 23, 8, 6, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 726
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057740 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057740
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057740/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057740
Building REAL300000057741
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057741'
/scratch/stefan/7769638/working/building/REAL300000057741 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057741

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057741/0 /scratch/stefan/7769638/working/building/REAL300000057741 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 774)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/774
`/scratch/stefan/7769638/working/3D/774' -> `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)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057741.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057741/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057741 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 42, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 1, 1, 1, 6, 16, 42, 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])
total number of confs: 122
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057741 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', '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, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 25, 25, 11, 11, 6, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 25, 11, 6, 1, 1, 1, 1] 47
rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 83
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057741 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057741
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057741/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057741
Building REAL300000057742
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057742'
/scratch/stefan/7769638/working/building/REAL300000057742 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057742

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057742/0 /scratch/stefan/7769638/working/building/REAL300000057742 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 775)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/775
`/scratch/stefan/7769638/working/3D/775' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1)

`REAL300000057742.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057742.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057742/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057742 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 11, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 6, 7, 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, 7, 2, 2, 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, 8, 12, 12, 12, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 8, 12, 26, 34, 34, 34, 34, 1, 1] 34
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27, 28, 37, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057742 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 11, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 6, 7, 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, 7, 2, 2, 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, 54, 56, 56, 54, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 54, 16, 6, 1, 1, 1, 1, 56, 56] 56
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 36, 37, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 155
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057742 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057742
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057742/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057742
Building REAL300000057743
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057743'
/scratch/stefan/7769638/working/building/REAL300000057743 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057743

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057743/0 /scratch/stefan/7769638/working/building/REAL300000057743 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 776)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/776
`/scratch/stefan/7769638/working/3D/776' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCC1=CC=CC=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057743.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057743.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057743/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057743 none CC(CCCCC1=CC=CC=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 13, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 112, 112, 112, 197, 201, 201, 197, 201, 201, 201, 201, 201, 55, 55, 55, 13, 13, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 112, 197, 201, 201, 201, 201] 201
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 41, 4, 38, 39, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47])
total number of confs: 680
number of broken/clashed sets: 189
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057743 none CC(CCCCC1=CC=CC=C1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 83, 87, 138, 199, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 83, 83, 109, 109, 135, 135, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 1006
number of broken/clashed sets: 189
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057743 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057743
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057743/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057743
Building REAL300000057744
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057744'
/scratch/stefan/7769638/working/building/REAL300000057744 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057744

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057744/0 /scratch/stefan/7769638/working/building/REAL300000057744 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 777)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/777
`/scratch/stefan/7769638/working/3D/777' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC3(CCOC3)OC3=CC=CC=C32)C=C1)

`REAL300000057744.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057744/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057744 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3(CCOC3)OC3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057744 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3(CCOC3)OC3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 24
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 44, 45, 26, 27, 28, 29, 30, 31])
total number of confs: 65
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057744 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057744
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057744/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057744
Building REAL300000057745
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057745'
/scratch/stefan/7769638/working/building/REAL300000057745 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057745

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057745/0 /scratch/stefan/7769638/working/building/REAL300000057745 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 778)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/778
`/scratch/stefan/7769638/working/3D/778' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=NN=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1)

`REAL300000057745.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057745.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057745/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057745 none CC(C)(C)C1=NN=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 55, 56, 56, 56, 56, 56, 56, 56, 56, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 22, 55, 56, 56, 56, 56] 56
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23] set([0, 2, 3, 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])
total number of confs: 166
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057745 none CC(C)(C)C1=NN=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 37, 37, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 37, 14, 7, 1, 1, 1, 1] 56
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057745 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057745
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057745/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057745
Building REAL300000057746
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057746'
/scratch/stefan/7769638/working/building/REAL300000057746 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057746

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057746/0 /scratch/stefan/7769638/working/building/REAL300000057746 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 779)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/779
`/scratch/stefan/7769638/working/3D/779' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NO1)

`REAL300000057746.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057746.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057746/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057746 none CCC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 46, 48, 48, 46, 47, 48, 48, 48, 48, 1, 1, 7, 8, 8, 7, 7, 1, 7, 23, 46, 48, 48, 48, 48] 69
rigid atoms, others: [1, 2, 3, 4, 5, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 156
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057746 none CCC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [69, 48, 48, 48, 36, 36, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 69, 69, 69, 69, 69, 48, 36, 14, 7, 1, 1, 1, 1] 69
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 219
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057746 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057746
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057746/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057746
Building REAL300000057747
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057747'
/scratch/stefan/7769638/working/building/REAL300000057747 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057747

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057747/0 /scratch/stefan/7769638/working/building/REAL300000057747 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 780)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/780
`/scratch/stefan/7769638/working/3D/780' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC23CCCC3)C=C1)

`REAL300000057747.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057747.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057747/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057747 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC23CCCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 43
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057747 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC23CCCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 16
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, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 40, 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
/scratch/stefan/7769638/working/building/REAL300000057747 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057747
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057747/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057747
Building REAL300000057748
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057748'
/scratch/stefan/7769638/working/building/REAL300000057748 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057748

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057748/0 /scratch/stefan/7769638/working/building/REAL300000057748 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 781)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/781
`/scratch/stefan/7769638/working/3D/781' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC23CCOC3)C=C1)

`REAL300000057748.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057748.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057748/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057748 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC23CCOC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 12, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16
rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 43
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057748 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC23CCOC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 12, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 16
rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 38, 37])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057748 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057748
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057748/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057748
Building REAL300000057749
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057749'
/scratch/stefan/7769638/working/building/REAL300000057749 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057749

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057749/0 /scratch/stefan/7769638/working/building/REAL300000057749 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 782)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/782
`/scratch/stefan/7769638/working/3D/782' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(Br)C=C2O)C=C1)

`REAL300000057749.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057749.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057749/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057749 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(Br)C=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 10, 10, 10, 30, 30, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 8, 10, 30, 43, 43, 86, 1, 1] 86
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 162
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057749 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(Br)C=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [47, 47, 47, 47, 47, 47, 47, 19, 18, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 18, 8, 1, 1, 2, 47, 47] 94
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32])
total number of confs: 135
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057749 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057749/1 /scratch/stefan/7769638/working/building/REAL300000057749 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 783)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/783
`/scratch/stefan/7769638/working/3D/783' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(Br)C=C2[O-])C=C1)

`REAL300000057749.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057749.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057749/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057749 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(Br)C=C2[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', '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, 11, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 7, 9, 15, 15, 15, 1, 1] 15
rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057749 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(Br)C=C2[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', '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, 11, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 8, 7, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 7, 3, 1, 1, 24, 24] 24
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 71
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057749 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057749
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057749/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057749/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057749
Building REAL300000057750
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057750'
/scratch/stefan/7769638/working/building/REAL300000057750 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057750

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057750/0 /scratch/stefan/7769638/working/building/REAL300000057750 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 784)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/784
`/scratch/stefan/7769638/working/3D/784' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C(C)C)C(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057750.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057750.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057750/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057750 none CC1=NN(C(C)C)C(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 5, 1, 1, 1, 1, 13, 13, 38, 38, 38, 88, 92, 92, 92, 92, 92, 92, 92, 92, 2, 2, 2, 5, 5, 5, 5, 6, 6, 6, 2, 2, 2, 13, 37, 88, 92, 92, 92, 92] 92
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 272
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057750 none CC1=NN(C(C)C)C(C)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [92, 92, 92, 92, 92, 92, 92, 92, 92, 50, 50, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 50, 18, 7, 1, 1, 1, 1] 92
rigid atoms, others: [41, 42, 43, 44, 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, 36, 37, 38, 39, 40])
total number of confs: 158
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057750 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057750
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057750/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057750
Building REAL300000057751
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057751'
/scratch/stefan/7769638/working/building/REAL300000057751 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057751

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057751/0 /scratch/stefan/7769638/working/building/REAL300000057751 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 785)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/785
`/scratch/stefan/7769638/working/3D/785' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN(CCF)C=C2)C=C1)

`REAL300000057751.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057751.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057751/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057751 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN(CCF)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'C.2', '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, 8, 1, 11, 8, 8, 1, 1, 8, 8, 5, 5, 15, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 46, 46, 81, 81, 81, 133, 133, 81, 81, 1, 1, 1, 1, 8, 14, 46, 133, 133, 133, 133, 81, 81, 1, 1] 133
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 399
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057751 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN(CCF)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'C.2', '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, 8, 1, 11, 8, 8, 1, 1, 8, 8, 5, 5, 15, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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: [82, 74, 82, 67, 82, 82, 67, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 9, 18, 1, 1, 82, 82, 82, 82, 67, 27, 9, 9, 9, 18, 18, 1, 1, 82, 82] 135
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 369
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057751 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057751
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057751/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057751
Building REAL300000057752
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057752'
/scratch/stefan/7769638/working/building/REAL300000057752 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057752

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057752/0 /scratch/stefan/7769638/working/building/REAL300000057752 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 786)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/786
`/scratch/stefan/7769638/working/3D/786' -> `0.mol2'
Preparing input files

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

`REAL300000057752.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057752.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057752/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057752 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.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: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 15, 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, 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
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 48, 48, 48, 48, 48, 48, 32, 32, 32, 14, 7, 1, 1, 1, 1, 48, 48, 48] 48
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 96
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057752 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.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: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 15, 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, 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
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [11, 1, 11, 11, 31, 31, 31, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 31, 48, 48, 48, 48, 48, 1, 1, 1] 48
rigid atoms, others: [32, 1, 34, 33, 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])
total number of confs: 141
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057752 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057752
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057752/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057752
Building REAL300000057753
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057753'
/scratch/stefan/7769638/working/building/REAL300000057753 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057753

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057753/0 /scratch/stefan/7769638/working/building/REAL300000057753 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 787)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/787
`/scratch/stefan/7769638/working/3D/787' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(O)C=CC=C2O)C=C1)

`REAL300000057753.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057753.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057753/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057753 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(O)C=CC=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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, 1, 1, 9, 11, 11, 11, 22, 22, 43, 43, 43, 22, 43, 43, 43, 1, 1, 1, 1, 9, 11, 22, 86, 43, 22, 43, 86, 1, 1] 172
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 301
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057753 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(O)C=CC=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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, 43, 43, 43, 24, 23, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 23, 7, 2, 1, 1, 1, 2, 43, 43] 172
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 125
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057753 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057753
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057753/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057753
Building REAL300000057754
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057754'
/scratch/stefan/7769638/working/building/REAL300000057754 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057754

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057754/0 /scratch/stefan/7769638/working/building/REAL300000057754 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 788)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/788
`/scratch/stefan/7769638/working/3D/788' -> `0.mol2'
Preparing input files

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

`REAL300000057754.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057754.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057754/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057754 none CNS(=O)(=O)CC(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 14, 11, 11, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 51, 83, 83, 22, 22, 22, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 51, 51, 22, 22, 22, 8, 6, 1, 1, 1, 1] 83
rigid atoms, others: [33, 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])
total number of confs: 340
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057754 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057754
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057754/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057754
Building REAL300000057755
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057755'
/scratch/stefan/7769638/working/building/REAL300000057755 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057755

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057755/0 /scratch/stefan/7769638/working/building/REAL300000057755 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 789)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/789
`/scratch/stefan/7769638/working/3D/789' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC(C)C)S1)

`REAL300000057755.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057755.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057755/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057755 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC(C)C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [36, 36, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 97, 97, 97, 97, 136, 136, 136, 97, 36, 36, 36, 17, 7, 1, 1, 1, 1, 97, 97, 136, 136, 136, 136, 136, 136, 136, 136, 136] 136
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 375
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057755 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC(C)C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [13, 1, 13, 13, 40, 40, 40, 90, 97, 97, 90, 94, 97, 97, 97, 97, 1, 1, 1, 1, 1, 4, 7, 7, 1, 13, 13, 13, 40, 88, 97, 97, 97, 97, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7] 136
rigid atoms, others: [1, 34, 35, 16, 17, 18, 19, 20, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 317
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057755 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057755
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057755/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057755
Building REAL300000057756
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057756'
/scratch/stefan/7769638/working/building/REAL300000057756 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057756

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057756/0 /scratch/stefan/7769638/working/building/REAL300000057756 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 790)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/790
`/scratch/stefan/7769638/working/3D/790' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC2=C(N1)SC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)=C2)

`REAL300000057756.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057756.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057756/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057756 none COC(=O)C1=CC2=C(N1)SC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)=C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 4, 4, 4, 1, 1, 6, 14, 39, 39, 39, 39, 39, 1] 71
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 39, 26, 30, 31] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 122
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057756 none COC(=O)C1=CC2=C(N1)SC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)=C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 39, 71, 39, 39, 39, 39, 39, 39, 26, 26, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 39, 71, 71, 71, 39, 39, 26, 10, 7, 1, 1, 1, 1, 39] 71
rigid atoms, others: [35, 36, 37, 38, 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, 39])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057756 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057756
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057756/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057756
Building REAL300000057757
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057757'
/scratch/stefan/7769638/working/building/REAL300000057757 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057757

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057757/0 /scratch/stefan/7769638/working/building/REAL300000057757 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 791)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/791
`/scratch/stefan/7769638/working/3D/791' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C=C1)

`REAL300000057757.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057757.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057757/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057757 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 11, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 25, 26, 27, 28] set([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: 45
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057757 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 11, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 25
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 40, 25, 26, 27, 28, 29, 30])
total number of confs: 65
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057757 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057757
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057757/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057757
Building REAL300000057758
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057758'
/scratch/stefan/7769638/working/building/REAL300000057758 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057758

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057758/0 /scratch/stefan/7769638/working/building/REAL300000057758 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 792)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/792
`/scratch/stefan/7769638/working/3D/792' -> `0.mol2'
Preparing input files

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

`REAL300000057758.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057758.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057758/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057758 none O=C([O-])C1=COC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 7, 25, 57, 57, 57, 57, 57, 1] 57
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057758 none O=C([O-])C1=COC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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, 34, 34, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 34, 12, 7, 1, 1, 1, 1, 57] 57
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: 108
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057758 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057758
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057758/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057758
Building REAL300000057759
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057759'
/scratch/stefan/7769638/working/building/REAL300000057759 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057759

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057759/0 /scratch/stefan/7769638/working/building/REAL300000057759 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 793)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/793
`/scratch/stefan/7769638/working/3D/793' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=N1)

`REAL300000057759.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057759.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057759/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057759 none CCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [8, 1, 1, 1, 1, 1, 11, 11, 36, 36, 36, 87, 102, 102, 95, 95, 102, 102, 102, 102, 1, 1, 1, 8, 8, 8, 8, 8, 1, 11, 36, 87, 102, 102, 102, 102, 2, 2, 2] 140
rigid atoms, others: [1, 2, 3, 4, 5, 20, 21, 22, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057759 none CCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [140, 102, 102, 102, 50, 50, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 140, 140, 140, 140, 140, 102, 50, 16, 7, 1, 1, 1, 1, 102, 102, 102] 140
rigid atoms, others: [32, 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, 36, 37, 38])
total number of confs: 402
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057759 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057759
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057759/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057759
Building REAL300000057760
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057760'
/scratch/stefan/7769638/working/building/REAL300000057760 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057760

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057760/0 /scratch/stefan/7769638/working/building/REAL300000057760 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 794)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/794
`/scratch/stefan/7769638/working/3D/794' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Cl)=CC(Br)=C2)C=C1)

`REAL300000057760.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057760.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057760/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057760 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Cl)=CC(Br)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 7, 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, 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, 9, 12, 12, 12, 26, 26, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 9, 12, 26, 51, 51, 51, 1, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057760 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Cl)=CC(Br)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 7, 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, 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, 23, 23, 23, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 23, 11, 1, 1, 1, 51, 51] 51
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 135
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057760 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057760
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057760/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057760
Building REAL300000057761
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057761'
/scratch/stefan/7769638/working/building/REAL300000057761 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057761

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057761/0 /scratch/stefan/7769638/working/building/REAL300000057761 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 795)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/795
`/scratch/stefan/7769638/working/3D/795' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C2=CC=CC=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1)

`REAL300000057761.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057761.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057761/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057761 none CC1=CC=C(C2=CC=CC=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 23, 23, 45, 45, 45, 95, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 23, 45, 95, 95, 95, 95, 95, 2, 2, 2, 1] 95
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 48, 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, 47])
total number of confs: 275
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057761 none CC1=CC=C(C2=CC=CC=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 56, 59, 59, 56, 56, 59, 59, 59, 59, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 25, 56, 59, 59, 59, 59, 5, 5, 5, 5] 95
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057761 none CC1=CC=C(C2=CC=CC=C2C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 59, 59, 59, 59, 59, 59, 27, 27, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 95, 95, 95, 95, 95, 95, 95, 95, 59, 59, 59, 59, 27, 14, 7, 1, 1, 1, 1, 95, 95, 95, 95] 95
rigid atoms, others: [41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48])
total number of confs: 174
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057761 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057761
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057761/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057761
Building REAL300000057762
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057762'
/scratch/stefan/7769638/working/building/REAL300000057762 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057762

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057762/0 /scratch/stefan/7769638/working/building/REAL300000057762 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 796)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/796
`/scratch/stefan/7769638/working/3D/796' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CC2)=N1)

`REAL300000057762.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057762.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057762/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057762 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 11, 11, 34, 34, 34, 80, 88, 88, 84, 88, 88, 88, 88, 88, 1, 1, 8, 8, 1, 2, 2, 2, 1, 11, 34, 80, 88, 88, 88, 88, 8, 8, 8, 8, 8] 111
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 272
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057762 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [88, 88, 88, 48, 48, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 88, 88, 111, 111, 88, 88, 88, 88, 88, 48, 17, 7, 1, 1, 1, 1, 111, 111, 111, 111, 111] 111
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39])
total number of confs: 236
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057762 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [8, 8, 8, 8, 8, 31, 31, 67, 67, 67, 108, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 8, 9, 9, 9, 8, 31, 67, 108, 111, 111, 111, 111, 1, 1, 1, 1, 1] 111
rigid atoms, others: [35, 36, 37, 38, 39, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 309
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057762 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057762
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057762/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057762
Building REAL300000057763
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057763'
/scratch/stefan/7769638/working/building/REAL300000057763 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057763

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057763/0 /scratch/stefan/7769638/working/building/REAL300000057763 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 797)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/797
`/scratch/stefan/7769638/working/3D/797' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(CC(F)(F)F)S2)C=C1)

`REAL300000057763.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057763.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057763/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057763 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(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', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 15, 15, 15, 14, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 19, 19, 19, 52, 52, 94, 94, 94, 94, 161, 161, 161, 161, 94, 1, 1, 1, 1, 11, 19, 52, 94, 161, 161, 1, 1] 161
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 23, 24, 25, 26] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 510
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057763 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(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', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 15, 15, 15, 14, 1, 1, 7, 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, 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: [88, 81, 88, 80, 88, 88, 75, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 8, 9, 8, 9, 1, 88, 88, 88, 88, 75, 33, 9, 1, 8, 8, 88, 88] 156
rigid atoms, others: [12, 13, 14, 15, 16, 17, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 304
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057763 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057763
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057763/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057763
Building REAL300000057764
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057764'
/scratch/stefan/7769638/working/building/REAL300000057764 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057764

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057764/0 /scratch/stefan/7769638/working/building/REAL300000057764 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 798)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/798
`/scratch/stefan/7769638/working/3D/798' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(C2=CSC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=N2)=C1)

`REAL300000057764.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057764.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057764/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057764 none COC1=CC=CC(C2=CSC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 52, 52, 109, 109, 109, 194, 201, 201, 199, 201, 201, 201, 201, 201, 13, 1, 3, 3, 3, 1, 1, 1, 13, 52, 109, 194, 201, 201, 201, 201, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 42, 7, 27, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 617
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057764 none COC1=CC=CC(C2=CSC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 37, 42, 42, 40, 42, 42, 42, 42, 42, 1, 13, 23, 23, 23, 12, 13, 13, 1, 6, 18, 37, 42, 42, 42, 42, 13] 201
rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057764 none COC1=CC=CC(C2=CSC(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
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, 42, 42, 42, 42, 22, 22, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 42, 201, 201, 201, 201, 201, 201, 201, 42, 22, 6, 6, 1, 1, 1, 1, 201] 201
rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 261
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057764 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057764
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057764/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057764
Building REAL300000057765
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057765'
/scratch/stefan/7769638/working/building/REAL300000057765 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057765

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057765/0 /scratch/stefan/7769638/working/building/REAL300000057765 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 799)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/799
`/scratch/stefan/7769638/working/3D/799' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Cl)C=C2[N+](=O)[O-])C=C1)

`REAL300000057765.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057765.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057765/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057765 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Cl)C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.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, 11, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 1, 7, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 18, 18, 18, 33, 33, 41, 41, 33, 40, 41, 41, 41, 41, 41, 1, 1, 1, 1, 12, 18, 33, 41, 41, 41, 1, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 23, 24, 25, 26] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057765 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Cl)C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.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, 11, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 1, 7, 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, 7, 3, 3, 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, 21, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 44, 44, 44, 44, 44, 21, 7, 1, 1, 1, 44, 44] 44
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 119
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057765 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057765
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057765/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057765
Building REAL300000057766
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057766'
/scratch/stefan/7769638/working/building/REAL300000057766 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057766

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057766/0 /scratch/stefan/7769638/working/building/REAL300000057766 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 800)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/800
`/scratch/stefan/7769638/working/3D/800' -> `0.mol2'
Preparing input files

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

`REAL300000057766.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057766.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057766/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057766 none CCCSCC(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 14, 5, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 75, 25, 25, 25, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 199, 75, 75, 25, 25, 25, 8, 6, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 663
number of broken/clashed sets: 177
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057766 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057766
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057766/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057766
Building REAL300000057767
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057767'
/scratch/stefan/7769638/working/building/REAL300000057767 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057767

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057767/0 /scratch/stefan/7769638/working/building/REAL300000057767 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 801)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/801
`/scratch/stefan/7769638/working/3D/801' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(Cl)C2=C1CCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057767.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057767.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057767/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057767 none COC1=CC=C(Cl)C2=C1CCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 40, 40, 39, 40, 40, 40, 40, 40, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 35, 40, 40, 40, 40] 40
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43])
total number of confs: 110
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057767 none COC1=CC=C(Cl)C2=C1CCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 40, 40, 40, 40, 40, 40, 40, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 15, 7, 1, 1, 1, 1] 40
rigid atoms, others: [40, 41, 42, 43, 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, 38, 39])
total number of confs: 75
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057767 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057767
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057767/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057767
Building REAL300000057768
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057768'
/scratch/stefan/7769638/working/building/REAL300000057768 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057768

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057768/0 /scratch/stefan/7769638/working/building/REAL300000057768 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 802)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/802
`/scratch/stefan/7769638/working/3D/802' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(O)=C1OC)

`REAL300000057768.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057768.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057768/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057768 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(O)=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 42, 47, 47, 42, 42, 47, 47, 47, 47, 1, 1, 1, 1, 4, 3, 3, 3, 1, 1, 6, 15, 42, 47, 47, 47, 47, 2, 5, 5, 5] 118
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 177
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057768 none COC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(O)=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 47, 47, 47, 47, 34, 34, 14, 14, 6, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 47, 47, 47, 47, 59, 59, 59, 59, 47, 47, 34, 14, 6, 1, 1, 1, 1, 94, 59, 59, 59] 118
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 236
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057768 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057768
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057768/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057768
Building REAL300000057769
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057769'
/scratch/stefan/7769638/working/building/REAL300000057769 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057769

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057769/0 /scratch/stefan/7769638/working/building/REAL300000057769 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 803)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/803
`/scratch/stefan/7769638/working/3D/803' -> `0.mol2'
Preparing input files

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

`REAL300000057769.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057769.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057769/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057769 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)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.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', 'C.3', 'F', 'F', 'F', '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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [15, 11, 11, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 19, 19, 11, 11, 19, 19, 19, 19, 19, 15, 15, 15, 15, 15, 5, 3, 1, 1, 1, 1, 19, 19, 19, 19] 21
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 113
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057769 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)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.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', 'C.3', 'F', 'F', 'F', '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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [7, 6, 1, 6, 6, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 10, 19, 19, 19, 19, 19, 1, 1, 1, 1] 21
rigid atoms, others: [2, 38, 39, 40, 41, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 67
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057769 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057769
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057769/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057769
Building REAL300000057770
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057770'
/scratch/stefan/7769638/working/building/REAL300000057770 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057770

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057770/0 /scratch/stefan/7769638/working/building/REAL300000057770 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 804)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/804
`/scratch/stefan/7769638/working/3D/804' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C2COCCN2C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057770.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057770/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057770 none COC(=O)C1=C2COCCN2C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 28, 28, 61, 69, 69, 66, 69, 69, 69, 69, 69, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 8, 27, 61, 69, 69, 69, 69, 1] 98
rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 44, 36, 27, 31] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 227
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057770 none COC(=O)C1=C2COCCN2C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 69, 98, 69, 69, 69, 69, 69, 69, 69, 27, 27, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 69, 98, 98, 98, 69, 69, 69, 69, 69, 69, 27, 6, 6, 1, 1, 1, 1, 69] 98
rigid atoms, others: [40, 41, 42, 43, 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, 38, 39, 44])
total number of confs: 217
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057770 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057770
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057770/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057770
Building REAL300000057771
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057771'
/scratch/stefan/7769638/working/building/REAL300000057771 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057771

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057771/0 /scratch/stefan/7769638/working/building/REAL300000057771 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 805)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/805
`/scratch/stefan/7769638/working/3D/805' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)C=C1)

`REAL300000057771.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057771.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057771/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057771 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 5, 5, 5, 9, 9, 5, 5, 15, 15, 15, 15, 15, 15, 15, 9, 9, 1, 1, 1, 1, 3, 5, 5, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 1, 1] 15
rigid atoms, others: [1, 3, 4, 5, 6, 7, 48, 49, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 61
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057771 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 4, 3, 4, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 9, 9, 9, 9, 9, 3, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 9, 9] 15
rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 46, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49])
total number of confs: 39
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057771 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15] 15
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49])
total number of confs: 41
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057771 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057771
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057771/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057771
Building REAL300000057772
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057772'
/scratch/stefan/7769638/working/building/REAL300000057772 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057772

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057772/0 /scratch/stefan/7769638/working/building/REAL300000057772 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 806)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/806
`/scratch/stefan/7769638/working/3D/806' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C2CC2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057772.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057772.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057772/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057772 none CN1N=C(C2CC2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 13, 13, 1, 1, 1, 10, 10, 35, 35, 35, 74, 83, 83, 79, 83, 83, 83, 83, 83, 2, 2, 2, 13, 13, 13, 13, 13, 1, 10, 35, 74, 83, 83, 83, 83] 119
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 32] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 273
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057772 none CN1N=C(C2CC2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 44, 44, 85, 85, 85, 117, 119, 119, 119, 119, 119, 119, 119, 119, 13, 13, 13, 1, 1, 1, 1, 1, 13, 44, 85, 117, 119, 119, 119, 119] 119
rigid atoms, others: [3, 4, 5, 6, 27, 28, 29, 30, 31] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 338
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057772 none CN1N=C(C2CC2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 83, 83, 83, 119, 119, 83, 38, 38, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 119, 119, 119, 119, 119, 83, 38, 15, 7, 1, 1, 1, 1] 119
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 278
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057772 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057772
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057772/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057772
Building REAL300000057773
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057773'
/scratch/stefan/7769638/working/building/REAL300000057773 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057773

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057773/0 /scratch/stefan/7769638/working/building/REAL300000057773 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 807)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/807
`/scratch/stefan/7769638/working/3D/807' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057773.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057773/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057773 none CCC1CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 31, 31, 29, 29, 31, 31, 31, 31, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 31, 31, 31, 31] 31
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 34, 37, 35, 36, 38, 28, 29, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 39, 40, 41, 42, 43, 44])
total number of confs: 102
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057773 none CCC1CCCCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 7, 1, 1, 1, 1] 31
rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 62
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057773 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057773
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057773/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057773
Building REAL300000057774
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057774'
/scratch/stefan/7769638/working/building/REAL300000057774 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057774

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057774/0 /scratch/stefan/7769638/working/building/REAL300000057774 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 808)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/808
`/scratch/stefan/7769638/working/3D/808' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(N2C=CN=C2)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057774.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057774/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057774 none CC1=CC(N2C=CN=C2)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 9, 9, 19, 19, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2, 1, 7, 7, 7, 1, 1, 9, 19, 38, 38, 38, 38, 38] 75
rigid atoms, others: [0, 1, 2, 3, 4, 9, 10, 11, 12, 34, 35, 30] set([5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 116
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057774 none CC1=CC(N2C=CN=C2)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 17, 17, 37, 37, 37, 75, 75, 75, 75, 75, 75, 75, 75, 75, 7, 7, 7, 7, 1, 1, 1, 7, 7, 16, 37, 75, 75, 75, 75, 75] 75
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 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, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057774 none CC1=CC(N2C=CN=C2)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 26, 26, 69, 69, 69, 70, 38, 38, 26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 69, 69, 70, 38, 38, 26, 14, 7, 1, 1, 1, 1] 75
rigid atoms, others: [39, 40, 41, 42, 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, 38])
total number of confs: 171
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057774 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057774
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057774/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057774
Building REAL300000057775
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057775'
/scratch/stefan/7769638/working/building/REAL300000057775 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057775

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057775/0 /scratch/stefan/7769638/working/building/REAL300000057775 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 809)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/809
`/scratch/stefan/7769638/working/3D/809' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057775.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057775.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057775/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057775 none NC(=O)C1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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: [8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 38, 48, 48, 38, 38, 48, 48, 48, 48, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 38, 48, 48, 48, 48, 1, 1] 66
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 38, 22, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 32, 33, 34, 35, 36, 37])
total number of confs: 191
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057775 none NC(=O)C1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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: [8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 48, 66, 48, 48, 48, 48, 48, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 66, 66, 48, 48, 48, 48, 48, 48, 48, 17, 7, 1, 1, 1, 1, 48, 48] 66
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, 38, 39])
total number of confs: 158
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057775 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057775
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057775/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057775
Building REAL300000057776
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057776'
/scratch/stefan/7769638/working/building/REAL300000057776 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057776

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057776/0 /scratch/stefan/7769638/working/building/REAL300000057776 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 810)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/810
`/scratch/stefan/7769638/working/3D/810' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCCC2C2=CC=CC=C2)C=C1)

`REAL300000057776.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057776.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057776/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057776 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCCC2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 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, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 6, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 6, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27
rigid atoms, others: [1, 3, 4, 5, 6, 7, 47, 48, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 54
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057776 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCCC2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 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, 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, 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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 28, 28] 28
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 75
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057776 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCCCC2C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 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, 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, 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, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 28, 28] 28
rigid atoms, others: [42, 43, 44, 45, 46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48])
total number of confs: 75
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057776 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057776
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057776/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057776
Building REAL300000057777
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057777'
/scratch/stefan/7769638/working/building/REAL300000057777 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057777

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057777/0 /scratch/stefan/7769638/working/building/REAL300000057777 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 811)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/811
`/scratch/stefan/7769638/working/3D/811' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2COC3=NC=CC=C23)C=C1)

`REAL300000057777.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057777/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057777 none O=C([O-])C1=CC=C(NC(=O)NN=C2COC3=NC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'O.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 3, 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, 1, 1, 1, 1, 1, 8, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 8, 10, 18, 18, 18, 18, 18, 1, 1] 18
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 40
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057777 none O=C([O-])C1=CC=C(NC(=O)NN=C2COC3=NC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'O.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 10, 9, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 9, 1, 1, 1, 1, 1, 18, 18] 18
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 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
/scratch/stefan/7769638/working/building/REAL300000057777 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057777
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057777/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057777
Building REAL300000057778
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057778'
/scratch/stefan/7769638/working/building/REAL300000057778 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057778

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057778/0 /scratch/stefan/7769638/working/building/REAL300000057778 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 812)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/812
`/scratch/stefan/7769638/working/3D/812' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Cl)=C2OCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1)

`REAL300000057778.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057778.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057778/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057778 none CC1=CC(Cl)=C2OCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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]
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, 9, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 1, 1, 1, 9, 19, 19, 19, 19, 19, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 28, 29, 30, 37] set([32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057778 none CC1=CC(Cl)=C2OCC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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]
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, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 11, 7, 1, 1, 1, 1, 19] 19
rigid atoms, others: [33, 34, 35, 36, 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, 37])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057778 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057778
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057778/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057778
Building REAL300000057779
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057779'
/scratch/stefan/7769638/working/building/REAL300000057779 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057779

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057779/0 /scratch/stefan/7769638/working/building/REAL300000057779 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 813)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/813
`/scratch/stefan/7769638/working/3D/813' -> `0.mol2'
Preparing input files

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

`REAL300000057779.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057779.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057779/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057779 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC=CC2=O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 23, 23, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 10, 23, 25, 25, 25, 25, 1, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 43
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057779 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC=CC2=O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 16, 15, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 15, 7, 1, 1, 1, 1, 31, 31] 31
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057779 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057779
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057779/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057779
Building REAL300000057780
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057780'
/scratch/stefan/7769638/working/building/REAL300000057780 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057780

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057780/0 /scratch/stefan/7769638/working/building/REAL300000057780 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 814)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/814
`/scratch/stefan/7769638/working/3D/814' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=NOC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057780.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057780.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057780/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057780 none CC(C)C1=NOC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 8, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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]
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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 31, 31, 31, 62, 64, 64, 63, 64, 64, 64, 64, 64, 3, 3, 3, 2, 3, 2, 3, 1, 10, 30, 62, 64, 64, 64, 64] 64
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057780 none CC(C)C1=NOC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 8, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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]
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, 38, 38, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 38, 12, 7, 1, 1, 1, 1] 64
rigid atoms, others: [34, 35, 36, 37, 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])
total number of confs: 118
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057780 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057780
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057780/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057780
Building REAL300000057781
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057781'
/scratch/stefan/7769638/working/building/REAL300000057781 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057781

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057781/0 /scratch/stefan/7769638/working/building/REAL300000057781 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 815)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/815
`/scratch/stefan/7769638/working/3D/815' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC1CCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057781.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057781.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057781/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057781 none CC(C)CC1CCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 20] 22
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 36, 38, 37] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44])
total number of confs: 63
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057781 none CC(C)CC1CCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 20, 20, 20, 20, 20, 20, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 20, 20, 20, 20, 20, 20, 20, 11, 7, 1, 1, 1, 1] 22
rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 58
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057781 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057781
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057781/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057781
Building REAL300000057782
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057782'
/scratch/stefan/7769638/working/building/REAL300000057782 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057782

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057782/0 /scratch/stefan/7769638/working/building/REAL300000057782 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 816)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/816
`/scratch/stefan/7769638/working/3D/816' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNN=C2C2=CC=C(Cl)O2)C=C1)

`REAL300000057782.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057782.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057782/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057782 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNN=C2C2=CC=C(Cl)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 12, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 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
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 38, 38, 78, 78, 78, 78, 78, 130, 130, 130, 130, 130, 1, 1, 1, 1, 8, 14, 38, 78, 78, 130, 130, 1, 1] 130
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: 227
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057782 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNN=C2C2=CC=C(Cl)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 12, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [68, 65, 68, 65, 68, 68, 61, 22, 22, 22, 11, 11, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 68, 68, 68, 68, 61, 22, 11, 1, 1, 9, 9, 68, 68] 80
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057782 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNN=C2C2=CC=C(Cl)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 12, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 80, 80, 80, 80, 76, 39, 39, 39, 28, 28, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 76, 39, 28, 9, 9, 1, 1, 80, 80] 80
rigid atoms, others: [33, 34, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 216
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057782 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057782
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057782/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057782
Building REAL300000057783
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057783'
/scratch/stefan/7769638/working/building/REAL300000057783 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057783

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057783/0 /scratch/stefan/7769638/working/building/REAL300000057783 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 817)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/817
`/scratch/stefan/7769638/working/3D/817' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C(=O)[O-])=C1)

`REAL300000057783.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057783.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057783/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057783 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 2, 2, 1, 2, 2, 2, 1, 1, 4, 4, 6, 6, 6, 6, 6, 1] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 24, 28, 29, 37] 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])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057783 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 1, 1, 1, 1, 6] 6
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37])
total number of confs: 17
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057783 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057783
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057783/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057783
Building REAL300000057784
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057784'
/scratch/stefan/7769638/working/building/REAL300000057784 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057784

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057784/0 /scratch/stefan/7769638/working/building/REAL300000057784 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 818)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/818
`/scratch/stefan/7769638/working/3D/818' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057784.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057784/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057784 none COC(=O)CCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.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', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 77, 8, 1, 1, 1, 1, 1, 1, 4, 4, 10, 11, 11, 26, 32, 32, 26, 30, 32, 32, 32, 32, 1, 77, 77, 77, 18, 18, 8, 8, 1, 1, 4, 10, 26, 32, 32, 32, 32] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 342
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057784 none COC(=O)CCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.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', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 94, 32, 32, 32, 32, 15, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 201, 201, 201, 150, 150, 94, 94, 32, 32, 15, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 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, 36, 37])
total number of confs: 801
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057784 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057784
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057784/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057784
Building REAL300000057785
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057785'
/scratch/stefan/7769638/working/building/REAL300000057785 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057785

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057785/0 /scratch/stefan/7769638/working/building/REAL300000057785 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 819)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/819
`/scratch/stefan/7769638/working/3D/819' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3CCC3)C2)C=C1)

`REAL300000057785.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057785.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057785/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057785 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3CCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 7, 11, 11, 11, 27, 27, 27, 27, 31, 31, 31, 27, 1, 1, 1, 1, 7, 11, 27, 27, 27, 31, 31, 31, 31, 31, 31, 31, 27, 27, 1, 1] 31
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 68
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057785 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3CCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 26, 27, 27, 26, 9, 8, 9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 27, 27, 27, 27, 26, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 27, 27] 31
rigid atoms, others: [36, 37, 10, 11, 12, 13, 14, 15, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 86
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057785 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3CCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 30, 31, 31, 30, 13, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 30, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31] 31
rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39])
total number of confs: 84
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057785 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057785
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057785/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057785
Building REAL300000057786
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057786'
/scratch/stefan/7769638/working/building/REAL300000057786 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057786

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057786/0 /scratch/stefan/7769638/working/building/REAL300000057786 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 820)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/820
`/scratch/stefan/7769638/working/3D/820' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OC(C)(C)C)

`REAL300000057786.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057786.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057786/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057786 none CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 10, 10, 32, 36, 36, 34, 34, 36, 36, 36, 36, 1, 1, 1, 4, 4, 7, 8, 8, 8, 2, 2, 2, 1, 1, 1, 9, 32, 36, 36, 36, 36, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9] 93
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 40, 39, 18, 19, 20, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 147
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057786 none CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [36, 36, 36, 36, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 61, 61, 93, 93, 93, 93, 36, 36, 36, 36, 36, 36, 11, 7, 1, 1, 1, 1, 36, 36, 93, 93, 93, 93, 93, 93, 93, 93, 93] 93
rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 212
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057786 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057786
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057786/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057786
Building REAL300000057787
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057787'
/scratch/stefan/7769638/working/building/REAL300000057787 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057787

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057787/0 /scratch/stefan/7769638/working/building/REAL300000057787 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 821)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/821
`/scratch/stefan/7769638/working/3D/821' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=COC2=C(C)C=CC=C12)

`REAL300000057787.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057787.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057787/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057787 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=COC2=C(C)C=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [30, 30, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 54, 54, 54, 54, 54, 54, 54, 54, 54, 30, 30, 30, 12, 7, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54] 54
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 103
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057787 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=COC2=C(C)C=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 11, 11, 33, 34, 34, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 33, 54, 54, 54, 54, 54, 1, 2, 2, 2, 1, 1, 1] 54
rigid atoms, others: [1, 35, 39, 40, 41, 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, 36, 37, 38])
total number of confs: 171
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057787 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057787
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057787/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057787
Building REAL300000057788
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057788'
/scratch/stefan/7769638/working/building/REAL300000057788 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057788

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057788/0 /scratch/stefan/7769638/working/building/REAL300000057788 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 822)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/822
`/scratch/stefan/7769638/working/3D/822' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=CC=C2F)C=C1)

`REAL300000057788.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057788.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057788/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057788 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=CC=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 37, 37, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 8, 14, 37, 51, 51, 51, 1, 1] 51
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 102
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057788 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=CC=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 60, 60, 60, 60, 21, 20, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 20, 6, 1, 1, 1, 60, 60] 60
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, 31])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057788 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057788
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057788/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057788
Building REAL300000057789
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057789'
/scratch/stefan/7769638/working/building/REAL300000057789 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057789

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057789/0 /scratch/stefan/7769638/working/building/REAL300000057789 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 823)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/823
`/scratch/stefan/7769638/working/3D/823' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CCOCC3)O2)C=C1)

`REAL300000057789.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057789.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057789/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057789 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CCOCC3)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 10, 16, 16, 16, 40, 40, 73, 73, 73, 73, 201, 201, 201, 201, 201, 73, 1, 1, 1, 1, 10, 16, 40, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 464
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057789 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CCOCC3)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 73, 61, 73, 73, 61, 29, 28, 29, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 73, 73, 73, 73, 61, 28, 8, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 73, 73] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 292
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057789 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=C(C3CCOCC3)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 186, 201, 186, 201, 201, 186, 117, 116, 117, 62, 62, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 186, 117, 63, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42])
total number of confs: 676
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057789 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057789
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057789/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057789
Building REAL300000057790
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057790'
/scratch/stefan/7769638/working/building/REAL300000057790 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057790

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057790/0 /scratch/stefan/7769638/working/building/REAL300000057790 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 824)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/824
`/scratch/stefan/7769638/working/3D/824' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1F)

`REAL300000057790.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057790.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057790/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057790 none COC1=NC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 4, 4, 4, 1, 1, 9, 17, 32, 32, 32, 32, 32] 32
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22, 23, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 96
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057790 none COC1=NC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 26, 26, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 26, 12, 7, 1, 1, 1, 1] 32
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])
total number of confs: 58
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057790 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057790
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057790/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057790
Building REAL300000057791
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057791'
/scratch/stefan/7769638/working/building/REAL300000057791 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057791

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057791/0 /scratch/stefan/7769638/working/building/REAL300000057791 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 825)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/825
`/scratch/stefan/7769638/working/3D/825' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(Cl)C=CC=C2Br)C=C1)

`REAL300000057791.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057791/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057791 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(Cl)C=CC=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 11, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 17, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 24, 24, 70, 70, 70, 64, 70, 70, 70, 1, 1, 1, 1, 10, 14, 24, 70, 70, 70, 1, 1] 70
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057791 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(Cl)C=CC=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 11, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 17, 1, 1, 7, 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, 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, 31, 31, 31, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 31, 11, 1, 1, 1, 70, 70] 70
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057791 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057791
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057791/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057791
Building REAL300000057792
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057792'
/scratch/stefan/7769638/working/building/REAL300000057792 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057792

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057792/0 /scratch/stefan/7769638/working/building/REAL300000057792 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 826)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/826
`/scratch/stefan/7769638/working/3D/826' -> `0.mol2'
Preparing input files

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

`REAL300000057792.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057792.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057792/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057792 none CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [77, 72, 32, 32, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 84, 84, 51, 84, 84, 84, 77, 77, 77, 77, 77, 72, 72, 15, 7, 1, 1, 1, 1, 84, 84, 55, 84] 98
rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 437
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057792 none CCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [32, 28, 9, 1, 9, 9, 30, 30, 30, 69, 84, 84, 78, 79, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 28, 28, 30, 69, 84, 84, 84, 84, 1, 1, 1, 1] 98
rigid atoms, others: [3, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 364
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057792 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057792
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057792/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057792
Building REAL300000057793
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057793'
/scratch/stefan/7769638/working/building/REAL300000057793 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057793

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057793/0 /scratch/stefan/7769638/working/building/REAL300000057793 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 827)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/827
`/scratch/stefan/7769638/working/3D/827' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C(Br)=C2F)C=C1)

`REAL300000057793.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057793/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057793 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C(Br)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 15, 1, 17, 1, 15, 1, 1, 7, 7, 6, 6, 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, 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, 8, 10, 10, 10, 22, 22, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 8, 10, 22, 28, 28, 1, 1] 28
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 54
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057793 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(F)C(Br)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 1, 15, 1, 17, 1, 15, 1, 1, 7, 7, 6, 6, 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, 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, 18, 18, 18, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 18, 11, 1, 1, 30, 30] 30
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057793 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057793
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057793/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057793
Building REAL300000057794
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057794'
/scratch/stefan/7769638/working/building/REAL300000057794 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057794

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057794/0 /scratch/stefan/7769638/working/building/REAL300000057794 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 828)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/828
`/scratch/stefan/7769638/working/3D/828' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CCC2CCCOC2)C=C1)

`REAL300000057794.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057794/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057794 none O=C([O-])C1=CC=C(NC(=O)NN=CCC2CCCOC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 12, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 20, 20, 20, 47, 47, 130, 201, 201, 201, 201, 200, 1, 1, 1, 1, 10, 20, 47, 130, 130, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 684
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057794 none O=C([O-])C1=CC=C(NC(=O)NN=CCC2CCCOC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 12, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 115, 115, 115, 54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 115, 54, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39])
total number of confs: 595
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057794 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057794
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057794/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057794
Building REAL300000057795
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057795'
/scratch/stefan/7769638/working/building/REAL300000057795 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057795

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057795/0 /scratch/stefan/7769638/working/building/REAL300000057795 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 829)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/829
`/scratch/stefan/7769638/working/3D/829' -> `0.mol2'
Preparing input files

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

`REAL300000057795.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057795.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057795/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057795 none O=C([O-])C1=CC=C(NC(=O)NN=CC2(C(F)(F)F)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 15, 15, 15, 5, 5, 1, 1, 7, 7, 6, 6, 7, 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, 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, 8, 11, 11, 11, 23, 23, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 8, 11, 23, 70, 70, 70, 70, 1, 1] 70
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 177
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057795 none O=C([O-])C1=CC=C(NC(=O)NN=CC2(C(F)(F)F)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 15, 15, 15, 5, 5, 1, 1, 7, 7, 6, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 75, 75, 75, 75, 33, 33, 33, 13, 13, 1, 1, 1, 2, 2, 2, 1, 1, 75, 75, 75, 75, 75, 32, 13, 1, 1, 1, 1, 75, 75] 75
rigid atoms, others: [12, 13, 14, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31, 32])
total number of confs: 215
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057795 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057795
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057795/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057795
Building REAL300000057796
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057796'
/scratch/stefan/7769638/working/building/REAL300000057796 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057796

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057796/0 /scratch/stefan/7769638/working/building/REAL300000057796 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 830)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/830
`/scratch/stefan/7769638/working/3D/830' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)N1C(=O)C2=CC=CC=C2C1=O)

`REAL300000057796.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057796.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057796/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057796 none CC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)N1C(=O)C2=CC=CC=C2C1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 3, 1, 1, 1, 1, 18, 18, 18, 18] 18
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 70
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057796 none CC(C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)N1C(=O)C2=CC=CC=C2C1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [5, 1, 5, 19, 19, 33, 33, 33, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 4, 19, 33, 70, 70, 70, 70, 70, 1, 1, 1, 1] 70
rigid atoms, others: [1, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 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: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057796 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057796
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057796/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057796
Building REAL300000057797
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057797'
/scratch/stefan/7769638/working/building/REAL300000057797 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057797

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057797/0 /scratch/stefan/7769638/working/building/REAL300000057797 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 831)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/831
`/scratch/stefan/7769638/working/3D/831' -> `0.mol2'
Preparing input files

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

`REAL300000057797.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057797.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057797/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057797 none COCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', '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, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [93, 85, 37, 37, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 74, 74, 37, 40, 74, 74, 93, 93, 93, 85, 85, 15, 7, 1, 1, 1, 1, 74, 74, 74, 74] 97
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 450
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057797 none COCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', '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, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [54, 27, 7, 1, 7, 7, 25, 25, 25, 60, 74, 74, 60, 65, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 27, 27, 25, 60, 74, 74, 74, 74, 1, 1, 1, 1] 97
rigid atoms, others: [3, 36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 391
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057797 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057797
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057797/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057797
Building REAL300000057798
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057798'
/scratch/stefan/7769638/working/building/REAL300000057798 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057798

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057798/0 /scratch/stefan/7769638/working/building/REAL300000057798 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 832)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/832
`/scratch/stefan/7769638/working/3D/832' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=NN(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057798.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057798.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057798/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057798 none COC(=O)C1=NN(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 1, 8, 8, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 28, 29, 29, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 9, 9, 9, 2, 2, 2, 11, 28, 53, 53, 53, 53, 53, 1] 80
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24, 38] set([0, 1, 3, 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])
total number of confs: 185
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057798 none COC(=O)C1=NN(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 1, 8, 8, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 53, 80, 53, 53, 53, 53, 27, 27, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 53, 80, 80, 80, 53, 53, 53, 27, 8, 6, 1, 1, 1, 1, 53] 80
rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 192
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057798 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057798
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057798/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057798
Building REAL300000057799
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057799'
/scratch/stefan/7769638/working/building/REAL300000057799 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057799

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057799/0 /scratch/stefan/7769638/working/building/REAL300000057799 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 833)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/833
`/scratch/stefan/7769638/working/3D/833' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1)

`REAL300000057799.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057799/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057799 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 35, 114, 114, 114, 114, 183, 201, 201, 114, 35, 35, 35, 16, 7, 1, 1, 1, 1, 114, 114, 183, 183, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 618
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057799 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 13, 41, 41, 41, 102, 114, 114, 102, 102, 114, 114, 114, 114, 1, 1, 1, 1, 1, 8, 27, 27, 1, 13, 13, 13, 41, 100, 114, 114, 114, 114, 1, 1, 8, 8, 27, 27, 27, 27, 27] 201
rigid atoms, others: [1, 34, 35, 16, 17, 18, 19, 20, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 455
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057799 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 103, 103, 148, 148, 148, 197, 201, 201, 197, 197, 201, 201, 201, 201, 27, 27, 27, 5, 1, 1, 1, 1, 27, 103, 103, 103, 148, 197, 201, 201, 201, 201, 27, 27, 5, 5, 1, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 42, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 588
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057799 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057799
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057799/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057799
Building REAL300000057800
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057800'
/scratch/stefan/7769638/working/building/REAL300000057800 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057800

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057800/0 /scratch/stefan/7769638/working/building/REAL300000057800 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 834)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/834
`/scratch/stefan/7769638/working/3D/834' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCCCO1)

`REAL300000057800.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057800.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057800/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057800 none COCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 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, 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: [17, 7, 1, 1, 1, 9, 9, 27, 27, 27, 62, 65, 65, 62, 62, 65, 65, 65, 65, 1, 1, 1, 1, 1, 18, 18, 18, 7, 7, 9, 27, 62, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1] 96
rigid atoms, others: [2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 251
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057800 none COCC1(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 65, 24, 24, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 65, 65, 65, 65, 65, 96, 96, 96, 96, 96, 24, 6, 6, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65] 96
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 322
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057800 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057800
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057800/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057800
Building REAL300000057801
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057801'
/scratch/stefan/7769638/working/building/REAL300000057801 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057801

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057801/0 /scratch/stefan/7769638/working/building/REAL300000057801 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 835)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/835
`/scratch/stefan/7769638/working/3D/835' -> `0.mol2'
Preparing input files

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

`REAL300000057801.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057801/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057801 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 44, 44, 44, 15, 7, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119] 119
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 294
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057801 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 43, 43, 43, 104, 119, 119, 104, 104, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 11, 11, 11, 43, 104, 119, 119, 119, 116, 1, 1, 4, 4, 1, 4, 4] 119
rigid atoms, others: [1, 36, 37, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42])
total number of confs: 418
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057801 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [27, 4, 27, 27, 68, 68, 68, 117, 119, 119, 117, 117, 119, 119, 119, 119, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 27, 27, 27, 68, 117, 119, 119, 119, 116, 4, 4, 1, 1, 1, 1, 1] 119
rigid atoms, others: [38, 39, 40, 41, 42, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 364
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057801 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057801
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057801/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057801
Building REAL300000057802
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057802'
/scratch/stefan/7769638/working/building/REAL300000057802 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057802

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057802/0 /scratch/stefan/7769638/working/building/REAL300000057802 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 836)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/836
`/scratch/stefan/7769638/working/3D/836' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN3C=CN=C3S2)C=C1)

`REAL300000057802.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057802.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057802/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057802 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN3C=CN=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 8, 1, 14, 1, 1, 7, 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, 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, 9, 10, 10, 10, 20, 20, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 9, 10, 20, 30, 30, 30, 1, 1] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 54
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057802 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN3C=CN=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 8, 1, 14, 1, 1, 7, 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, 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, 19, 18, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 18, 8, 1, 1, 1, 30, 30] 30
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 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
/scratch/stefan/7769638/working/building/REAL300000057802 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057802
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057802/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057802
Building REAL300000057803
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057803'
/scratch/stefan/7769638/working/building/REAL300000057803 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057803

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057803/0 /scratch/stefan/7769638/working/building/REAL300000057803 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 837)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/837
`/scratch/stefan/7769638/working/3D/837' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C(C(C)(C)C)O1)

`REAL300000057803.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057803.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057803/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057803 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C(C(C)(C)C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 12, 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, 7, 4, 7, 6, 4, 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, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 10, 10, 32, 33, 33, 74, 77, 77, 74, 74, 77, 77, 77, 77, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 10, 32, 74, 77, 77, 77, 77, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 77
rigid atoms, others: [0, 1, 2, 3, 35, 18, 19, 20, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 258
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057803 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C(C(C)(C)C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 12, 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, 7, 4, 7, 6, 4, 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, 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, 38, 38, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 38, 14, 7, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77] 77
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 131
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057803 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057803
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057803/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057803
Building REAL300000057804
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057804'
/scratch/stefan/7769638/working/building/REAL300000057804 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057804

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057804/0 /scratch/stefan/7769638/working/building/REAL300000057804 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 838)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/838
`/scratch/stefan/7769638/working/3D/838' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057804.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057804.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057804/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057804 none C=CC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 29, 33, 33, 29, 29, 33, 33, 33, 33, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 29, 33, 33, 33, 33, 1, 1] 33
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 38, 39, 21, 25, 26, 27, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 32, 33, 34, 35, 36, 37])
total number of confs: 115
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057804 none C=CC1CCCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 7, 1, 1, 1, 1, 33, 33] 33
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 65
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057804 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057804
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057804/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057804
Building REAL300000057805
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057805'
/scratch/stefan/7769638/working/building/REAL300000057805 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057805

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057805/0 /scratch/stefan/7769638/working/building/REAL300000057805 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 839)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/839
`/scratch/stefan/7769638/working/3D/839' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Cl)C=C2O)C=C1)

`REAL300000057805.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057805.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057805/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057805 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Cl)C=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 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, 4, 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: [2, 1, 2, 1, 1, 1, 1, 1, 6, 8, 8, 8, 18, 18, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 6, 8, 18, 22, 22, 22, 44, 1, 1] 44
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 88
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057805 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(Cl)C=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 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, 4, 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, 22, 22, 22, 10, 10, 10, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 10, 8, 1, 1, 1, 2, 22, 22] 44
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 59
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057805 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057805
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057805/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057805
Building REAL300000057806
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057806'
/scratch/stefan/7769638/working/building/REAL300000057806 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057806

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057806/0 /scratch/stefan/7769638/working/building/REAL300000057806 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 840)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/840
`/scratch/stefan/7769638/working/3D/840' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)SC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057806.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057806/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057806 none CC1=C(C)SC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 2, 2, 2, 2, 2, 2, 7, 15, 37, 37, 37, 37, 37] 37
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21] set([7, 8, 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: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057806 none CC1=C(C)SC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 26, 26, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 37, 37, 26, 8, 5, 1, 1, 1, 1] 37
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 72
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057806 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057806
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057806/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057806
Building REAL300000057807
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057807'
/scratch/stefan/7769638/working/building/REAL300000057807 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057807

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057807/0 /scratch/stefan/7769638/working/building/REAL300000057807 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 841)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/841
`/scratch/stefan/7769638/working/3D/841' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3=CC=CC=C3)N=N2)C=C1)

`REAL300000057807.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057807.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057807/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057807 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3=CC=CC=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 16, 16, 41, 41, 68, 68, 68, 194, 201, 201, 201, 201, 201, 68, 68, 1, 1, 1, 1, 8, 16, 41, 68, 194, 194, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 623
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057807 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3=CC=CC=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 55, 67, 55, 67, 67, 55, 21, 21, 21, 8, 8, 1, 1, 1, 1, 1, 9, 19, 19, 13, 19, 19, 1, 1, 67, 67, 67, 67, 55, 20, 8, 1, 9, 9, 19, 19, 19, 19, 19, 67, 67] 201
rigid atoms, others: [32, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057807 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3=CC=CC=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 196, 201, 196, 201, 201, 196, 105, 105, 105, 63, 63, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 201, 196, 105, 63, 19, 4, 4, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41])
total number of confs: 609
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057807 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057807
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057807/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057807
Building REAL300000057808
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057808'
/scratch/stefan/7769638/working/building/REAL300000057808 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057808

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057808/0 /scratch/stefan/7769638/working/building/REAL300000057808 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 842)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/842
`/scratch/stefan/7769638/working/3D/842' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(O)=CC(Cl)=C2)C=C1)

`REAL300000057808.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057808/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057808 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(O)=CC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 12, 1, 1, 16, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 27, 27, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 10, 14, 27, 48, 96, 48, 48, 1, 1] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057808 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(O)=CC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 12, 1, 1, 16, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 27, 26, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 26, 8, 1, 2, 1, 1, 48, 48] 96
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 29, 32, 33])
total number of confs: 131
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057808 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057808
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057808/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057808
Building REAL300000057809
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057809'
/scratch/stefan/7769638/working/building/REAL300000057809 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057809

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057809/0 /scratch/stefan/7769638/working/building/REAL300000057809 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 843)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/843
`/scratch/stefan/7769638/working/3D/843' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NOC(C3CC3)=C2)C=C1)

`REAL300000057809.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057809.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057809/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057809 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NOC(C3CC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 1, 11, 8, 8, 1, 1, 8, 12, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 12, 12, 12, 43, 43, 55, 55, 55, 55, 83, 83, 55, 1, 1, 1, 1, 9, 12, 43, 83, 83, 83, 83, 83, 55, 1, 1] 83
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 198
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057809 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NOC(C3CC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 1, 11, 8, 8, 1, 1, 8, 12, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [61, 59, 61, 53, 61, 61, 53, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 13, 13, 1, 61, 61, 61, 61, 53, 24, 7, 13, 13, 13, 13, 13, 1, 61, 61] 99
rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 220
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057809 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NOC(C3CC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 1, 11, 8, 8, 1, 1, 8, 12, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [97, 97, 97, 96, 97, 97, 96, 69, 69, 69, 36, 36, 12, 11, 11, 12, 1, 1, 1, 1, 12, 97, 97, 97, 97, 96, 69, 36, 1, 1, 1, 1, 1, 12, 97, 97] 97
rigid atoms, others: [32, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35])
total number of confs: 275
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057809 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057809
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057809/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057809
Building REAL300000057810
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057810'
/scratch/stefan/7769638/working/building/REAL300000057810 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057810

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057810/0 /scratch/stefan/7769638/working/building/REAL300000057810 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 844)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/844
`/scratch/stefan/7769638/working/3D/844' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Br)=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057810.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057810/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057810 none CC1=CC(Br)=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 17, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 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
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, 12, 12, 32, 33, 33, 54, 54, 54, 54, 54, 54, 54, 54, 54, 2, 2, 2, 1, 1, 12, 32, 54, 54, 54, 54, 54] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057810 none CC1=CC(Br)=CN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 17, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 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
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, 24, 24, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 54, 54, 54, 54, 54, 24, 12, 7, 1, 1, 1, 1] 54
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 97
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057810 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057810
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057810/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057810
Building REAL300000057811
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057811'
/scratch/stefan/7769638/working/building/REAL300000057811 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057811

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057811/0 /scratch/stefan/7769638/working/building/REAL300000057811 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 845)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/845
`/scratch/stefan/7769638/working/3D/845' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1C(=O)[O-])

`REAL300000057811.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057811.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057811/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057811 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', '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.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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 2, 2, 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
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 36, 36, 36, 83, 97, 97, 83, 83, 97, 97, 97, 97, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 12, 36, 83, 97, 97, 97, 97, 1, 1] 114
rigid atoms, others: [1, 2, 3, 4, 5, 38, 20, 21, 22, 23, 29, 37] 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])
total number of confs: 346
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057811 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', '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.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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 2, 2, 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
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [114, 97, 97, 97, 43, 43, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 97, 97, 97, 97, 114, 114, 114, 114, 114, 97, 43, 18, 7, 1, 1, 1, 1, 97, 97] 114
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 267
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057811 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057811
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057811/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057811
Building REAL300000057812
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057812'
/scratch/stefan/7769638/working/building/REAL300000057812 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057812

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057812/0 /scratch/stefan/7769638/working/building/REAL300000057812 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 846)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/846
`/scratch/stefan/7769638/working/3D/846' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OC(C)(C)C)

`REAL300000057812.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057812/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057812 none CCC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 1, 1, 1, 1, 1, 9, 10, 10, 32, 37, 37, 36, 36, 37, 37, 37, 37, 1, 1, 1, 5, 5, 11, 11, 11, 11, 3, 3, 3, 3, 3, 1, 1, 1, 9, 32, 37, 37, 37, 37, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11] 106
rigid atoms, others: [19, 1, 2, 3, 4, 5, 6, 33, 42, 43, 34, 35, 20, 21] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 126
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057812 none CCC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [40, 37, 37, 37, 37, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 65, 65, 106, 106, 106, 106, 40, 40, 40, 40, 40, 37, 37, 37, 11, 7, 1, 1, 1, 1, 37, 37, 106, 106, 106, 106, 106, 106, 106, 106, 106] 106
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 17, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 257
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057812 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057812
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057812/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057812
Building REAL300000057813
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057813'
/scratch/stefan/7769638/working/building/REAL300000057813 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057813

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057813/0 /scratch/stefan/7769638/working/building/REAL300000057813 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 847)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/847
`/scratch/stefan/7769638/working/3D/847' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOCC23CCC3)C=C1)

`REAL300000057813.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057813.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057813/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057813 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOCC23CCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 8, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 52
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057813 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOCC23CCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19
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, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 40, 21, 22, 23, 24, 25, 26])
total number of confs: 47
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057813 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057813
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057813/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057813
Building REAL300000057814
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057814'
/scratch/stefan/7769638/working/building/REAL300000057814 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057814

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057814/0 /scratch/stefan/7769638/working/building/REAL300000057814 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 848)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/848
`/scratch/stefan/7769638/working/3D/848' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C(F)F)

`REAL300000057814.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057814/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057814 none CN1N=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C(F)F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 11, 11, 11, 24, 27, 27, 24, 26, 27, 27, 27, 27, 1, 1, 6, 6, 2, 2, 2, 4, 11, 24, 27, 27, 27, 27, 6] 33
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])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057814 none CN1N=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C(F)F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 19, 19, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 33, 33, 27, 27, 27, 19, 12, 7, 1, 1, 1, 1, 33] 33
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057814 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057814
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057814/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057814
Building REAL300000057815
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057815'
/scratch/stefan/7769638/working/building/REAL300000057815 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057815

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057815/0 /scratch/stefan/7769638/working/building/REAL300000057815 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 849)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/849
`/scratch/stefan/7769638/working/3D/849' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(S(=O)(=O)C(F)F)=C2)C=C1)

`REAL300000057815.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057815.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057815/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057815 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(S(=O)(=O)C(F)F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 3, 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, 9, 14, 14, 14, 40, 40, 133, 133, 76, 133, 133, 201, 201, 201, 201, 201, 133, 1, 1, 1, 1, 9, 14, 40, 133, 133, 111, 201, 133, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 25, 26, 27, 28, 37] set([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])
total number of confs: 776
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057815 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(S(=O)(=O)C(F)F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 3, 3, 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: [76, 71, 76, 65, 76, 76, 65, 25, 24, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 15, 1, 76, 76, 76, 76, 65, 24, 8, 1, 1, 1, 14, 1, 76, 76] 113
rigid atoms, others: [32, 33, 34, 36, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 37, 38])
total number of confs: 307
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057815 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057815
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057815/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057815
Building REAL300000057816
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057816'
/scratch/stefan/7769638/working/building/REAL300000057816 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057816

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057816/0 /scratch/stefan/7769638/working/building/REAL300000057816 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 850)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/850
`/scratch/stefan/7769638/working/3D/850' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCOCC2)=NN1C)

`REAL300000057816.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057816/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057816 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCOCC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 8, 5, 7, 7, 7, 6, 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, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 35, 93, 93, 93, 196, 196, 196, 196, 196, 93, 93, 93, 35, 35, 35, 16, 7, 1, 1, 1, 1, 93, 196, 196, 196, 196, 196, 196, 196, 196, 196, 93, 93, 93] 196
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 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: 481
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057816 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCOCC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 8, 5, 7, 7, 7, 6, 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, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 32, 32, 32, 83, 93, 93, 83, 90, 93, 93, 93, 93, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 10, 10, 10, 32, 83, 93, 93, 93, 93, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2] 196
rigid atoms, others: [1, 37, 16, 17, 18, 19, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 325
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057816 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCOCC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 8, 5, 7, 7, 7, 6, 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, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [78, 13, 78, 78, 130, 130, 130, 194, 196, 196, 194, 196, 196, 196, 196, 196, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 78, 78, 78, 130, 194, 196, 196, 196, 196, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 196
rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49])
total number of confs: 554
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057816 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057816
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057816/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057816
Building REAL300000057817
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057817'
/scratch/stefan/7769638/working/building/REAL300000057817 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057817

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057817/0 /scratch/stefan/7769638/working/building/REAL300000057817 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 851)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/851
`/scratch/stefan/7769638/working/3D/851' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1OC2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C2C1C)

`REAL300000057817.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057817/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057817 none CC1OC2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C2C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 24, 25, 25, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 24, 48, 48, 48, 48, 48, 1, 1, 2, 2, 2] 48
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 22, 23, 24, 25, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43])
total number of confs: 145
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057817 none CC1OC2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C2C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 27, 27, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 27, 14, 7, 1, 1, 1, 1, 48, 48, 48, 48, 48] 48
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057817 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057817
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057817/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057817
Building REAL300000057818
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057818'
/scratch/stefan/7769638/working/building/REAL300000057818 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057818

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057818/0 /scratch/stefan/7769638/working/building/REAL300000057818 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 852)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/852
`/scratch/stefan/7769638/working/3D/852' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC(F)F)

`REAL300000057818.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057818.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057818/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057818 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC(F)F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 33, 33, 33, 68, 88, 88, 77, 77, 88, 88, 88, 88, 1, 1, 1, 8, 42, 42, 2, 2, 2, 1, 1, 10, 33, 68, 88, 88, 88, 88, 1, 42] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 39])
total number of confs: 434
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057818 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1OC(F)F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 33, 33, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 88, 88, 88, 186, 201, 201, 88, 88, 88, 88, 88, 33, 15, 7, 1, 1, 1, 1, 88, 201] 201
rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 388
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057818 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057818
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057818/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057818
Building REAL300000057819
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057819'
/scratch/stefan/7769638/working/building/REAL300000057819 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057819

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057819/0 /scratch/stefan/7769638/working/building/REAL300000057819 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 853)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/853
`/scratch/stefan/7769638/working/3D/853' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1C)

`REAL300000057819.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057819.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057819/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057819 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 25, 26, 26, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 2, 2, 2, 1, 1, 9, 25, 58, 58, 58, 58, 58, 2, 2, 2] 58
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057819 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 33, 33, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 33, 13, 7, 1, 1, 1, 1, 58, 58, 58] 58
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057819 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057819
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057819/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057819
Building REAL300000057820
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057820'
/scratch/stefan/7769638/working/building/REAL300000057820 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057820

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057820/0 /scratch/stefan/7769638/working/building/REAL300000057820 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 854)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/854
`/scratch/stefan/7769638/working/3D/854' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1)

`REAL300000057820.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057820.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057820/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057820 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 6, 6, 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, 2, 2, 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, 8, 12, 12, 12, 28, 28, 42, 42, 42, 28, 28, 42, 42, 42, 42, 42, 1, 1, 1, 1, 8, 12, 28, 42, 42, 1, 1] 42
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057820 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 6, 6, 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, 2, 2, 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, 21, 20, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 42, 42, 42, 42, 42, 20, 7, 1, 1, 42, 42] 42
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 129
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057820 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057820
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057820/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057820
Building REAL300000057821
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057821'
/scratch/stefan/7769638/working/building/REAL300000057821 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057821

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057821/0 /scratch/stefan/7769638/working/building/REAL300000057821 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 855)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/855
`/scratch/stefan/7769638/working/3D/855' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057821.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057821/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057821 none CC1=C(C(=O)[O-])NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 5, 5, 11, 11, 11, 31, 37, 37, 34, 37, 37, 37, 37, 37, 1, 2, 2, 2, 1, 5, 11, 31, 37, 37, 37, 37, 1] 37
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 35, 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])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057821 none CC1=C(C(=O)[O-])NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 37, 32, 32, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 32, 10, 7, 1, 1, 1, 1, 37] 37
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 66
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057821 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057821
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057821/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057821
Building REAL300000057822
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057822'
/scratch/stefan/7769638/working/building/REAL300000057822 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057822

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057822/0 /scratch/stefan/7769638/working/building/REAL300000057822 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 856)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/856
`/scratch/stefan/7769638/working/3D/856' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(Br)=C2F)C=C1)

`REAL300000057822.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057822.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057822/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057822 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(Br)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 8, 1, 17, 1, 15, 1, 1, 7, 7, 6, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 10, 10, 10, 22, 22, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 8, 10, 22, 29, 29, 1, 1] 29
rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057822 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=NC(Br)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 1, 8, 1, 17, 1, 15, 1, 1, 7, 7, 6, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 17, 11, 1, 1, 29, 29] 29
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057822 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057822
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057822/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057822
Building REAL300000057823
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057823'
/scratch/stefan/7769638/working/building/REAL300000057823 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057823

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057823/0 /scratch/stefan/7769638/working/building/REAL300000057823 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 857)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/857
`/scratch/stefan/7769638/working/3D/857' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=C(F)C=CC(Cl)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057823.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057823/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057823 none NC1=C(F)C=CC(Cl)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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: [8, 1, 1, 15, 1, 1, 1, 16, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 10, 26, 38, 38, 38, 38, 38] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27] set([32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057823 none NC1=C(F)C=CC(Cl)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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: [8, 1, 1, 15, 1, 1, 1, 16, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 24, 24, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 24, 14, 7, 1, 1, 1, 1] 38
rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057823 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057823
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057823/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057823
Building REAL300000057824
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057824'
/scratch/stefan/7769638/working/building/REAL300000057824 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057824

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057824/0 /scratch/stefan/7769638/working/building/REAL300000057824 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 858)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/858
`/scratch/stefan/7769638/working/3D/858' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C2CC2)=C1O)

`REAL300000057824.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057824.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057824/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057824 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C2CC2)=C1O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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
366  conformations in input
total number of sets (complete confs): 366
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 13, 13, 45, 45, 45, 109, 129, 129, 118, 118, 129, 129, 129, 129, 1, 1, 1, 6, 6, 1, 1, 4, 4, 4, 1, 13, 45, 109, 129, 129, 129, 129, 1, 6, 6, 6, 6, 6, 2] 366
rigid atoms, others: [1, 2, 3, 4, 5, 38, 20, 21, 22, 25, 26, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44])
total number of confs: 432
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057824 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C2CC2)=C1O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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
366  conformations in input
total number of sets (complete confs): 366
using faster count positions algorithm for large data
unique positions, atoms: [166, 129, 129, 129, 43, 43, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 183, 183, 129, 129, 166, 166, 166, 129, 43, 18, 7, 1, 1, 1, 1, 129, 183, 183, 183, 183, 183, 258] 366
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, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 733
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057824 none COC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C2CC2)=C1O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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
366  conformations in input
total number of sets (complete confs): 366
using faster count positions algorithm for large data
unique positions, atoms: [16, 6, 6, 6, 6, 6, 43, 43, 95, 95, 95, 176, 183, 183, 181, 181, 183, 183, 183, 183, 6, 1, 1, 1, 1, 6, 6, 16, 16, 16, 6, 43, 95, 176, 183, 183, 183, 183, 6, 1, 1, 1, 1, 1, 12] 366
rigid atoms, others: [39, 40, 41, 42, 43, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44])
total number of confs: 550
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057824 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057824
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057824/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057824
Building REAL300000057825
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057825'
/scratch/stefan/7769638/working/building/REAL300000057825 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057825

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057825/0 /scratch/stefan/7769638/working/building/REAL300000057825 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 859)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/859
`/scratch/stefan/7769638/working/3D/859' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC(F)C1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057825.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057825/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057825 none CC1(C)CCC(F)C1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 5, 5, 15, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 4, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 4, 16, 16, 16, 16, 16] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057825 none CC1(C)CCC(F)C1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 5, 5, 15, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 7, 1, 1, 1, 1] 16
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057825 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057825
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057825/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057825
Building REAL300000057826
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057826'
/scratch/stefan/7769638/working/building/REAL300000057826 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057826

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057826/0 /scratch/stefan/7769638/working/building/REAL300000057826 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 860)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/860
`/scratch/stefan/7769638/working/3D/860' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC2=C1CCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057826.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057826.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057826/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057826 none CC1=CC=CC2=C1CCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', '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.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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 8, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 49
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057826 none CC1=CC=CC2=C1CCCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', '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.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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 7, 1, 1, 1, 1] 17
rigid atoms, others: [39, 40, 41, 42, 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, 36, 37, 38])
total number of confs: 44
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057826 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057826
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057826/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057826
Building REAL300000057827
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057827'
/scratch/stefan/7769638/working/building/REAL300000057827 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057827

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057827/0 /scratch/stefan/7769638/working/building/REAL300000057827 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 861)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/861
`/scratch/stefan/7769638/working/3D/861' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057827.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057827.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057827/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057827 none CC(C)CC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.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.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [7, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 72, 78, 78, 76, 78, 78, 78, 78, 78, 8, 8, 8, 8, 8, 8, 8, 6, 6, 1, 1, 1, 1, 11, 29, 72, 78, 78, 78, 78] 106
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 36, 37] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 250
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057827 none CC(C)CC1=CC=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.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.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 78, 78, 78, 78, 78, 78, 30, 30, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 106, 106, 106, 106, 106, 106, 106, 106, 106, 78, 78, 78, 78, 30, 15, 7, 1, 1, 1, 1] 106
rigid atoms, others: [41, 42, 43, 44, 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, 36, 37, 38, 39, 40])
total number of confs: 289
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057827 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057827
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057827/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057827
Building REAL300000057828
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057828'
/scratch/stefan/7769638/working/building/REAL300000057828 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057828

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057828/0 /scratch/stefan/7769638/working/building/REAL300000057828 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 862)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/862
`/scratch/stefan/7769638/working/3D/862' -> `0.mol2'
Preparing input files

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

`REAL300000057828.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057828/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057828 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 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, 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: [37, 18, 18, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 62, 62, 62, 62, 62, 62, 62, 37, 37, 37, 37, 37, 8, 6, 1, 1, 1, 1, 62, 62, 62, 62, 62] 71
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40])
total number of confs: 194
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057828 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 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, 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: [31, 12, 1, 12, 12, 34, 34, 34, 56, 62, 62, 60, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 34, 56, 62, 62, 62, 62, 1, 2, 2, 1, 1] 71
rigid atoms, others: [2, 36, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 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, 37, 38])
total number of confs: 285
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057828 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057828
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057828/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057828
Building REAL300000057829
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057829'
/scratch/stefan/7769638/working/building/REAL300000057829 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057829

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057829/0 /scratch/stefan/7769638/working/building/REAL300000057829 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 863)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/863
`/scratch/stefan/7769638/working/3D/863' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1S(C)(=O)=O)

`REAL300000057829.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057829/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057829 none CN1N=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1S(C)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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
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, 4, 4, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 5, 5, 5, 2, 2, 2, 1, 4, 6, 14, 14, 14, 14, 14, 5, 5, 5] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 58
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057829 none CN1N=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1S(C)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 8, 8, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 14, 14, 19, 19, 19, 14, 14, 14, 14, 8, 8, 6, 1, 1, 1, 1, 19, 19, 19] 19
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 64
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057829 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057829
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057829/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057829
Building REAL300000057830
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057830'
/scratch/stefan/7769638/working/building/REAL300000057830 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057830

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057830/0 /scratch/stefan/7769638/working/building/REAL300000057830 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 864)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/864
`/scratch/stefan/7769638/working/3D/864' -> `0.mol2'
Preparing input files

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

`REAL300000057830.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057830/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057830 none CC(C)C1=CC=C(O)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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]
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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 22, 23, 23, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 5, 5, 5, 4, 5, 5, 5, 1, 1, 2, 9, 22, 52, 52, 52, 52, 52, 1] 112
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 8, 9, 42, 7, 24] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 169
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057830 none CC(C)C1=CC=C(O)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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]
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, 52, 56, 52, 32, 52, 51, 52, 29, 29, 15, 15, 6, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 52, 56, 56, 56, 56, 56, 56, 56, 52, 52, 104, 29, 15, 6, 1, 1, 1, 1, 52] 112
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 313
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057830 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057830
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057830/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057830
Building REAL300000057831
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057831'
/scratch/stefan/7769638/working/building/REAL300000057831 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057831

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057831/0 /scratch/stefan/7769638/working/building/REAL300000057831 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 865)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/865
`/scratch/stefan/7769638/working/3D/865' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C=NN1C)

`REAL300000057831.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057831.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057831/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057831 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 8, 8, 5, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 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: [20, 20, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 47, 47, 47, 47, 47, 47, 20, 20, 20, 12, 7, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47] 47
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 88
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057831 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 8, 8, 5, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 27, 27, 27, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 27, 47, 47, 47, 47, 47, 2, 2, 2, 1, 2, 2, 2] 47
rigid atoms, others: [1, 35, 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, 36, 37, 38])
total number of confs: 135
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057831 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057831
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057831/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057831
Building REAL300000057832
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057832'
/scratch/stefan/7769638/working/building/REAL300000057832 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057832

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057832/0 /scratch/stefan/7769638/working/building/REAL300000057832 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 866)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/866
`/scratch/stefan/7769638/working/3D/866' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(F)(F)F)NN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057832.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057832/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057832 none CC1=C(C(F)(F)F)NN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 5, 15, 15, 15, 8, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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, 2, 2, 2, 1, 1, 1, 1, 8, 8, 16, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 8, 16, 31, 31, 31, 31, 31] 31
rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 28] set([4, 5, 6, 11, 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: 97
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057832 none CC1=C(C(F)(F)F)NN=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 5, 15, 15, 15, 8, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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, 22, 22, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 22, 10, 7, 1, 1, 1, 1] 31
rigid atoms, others: [32, 33, 34, 35, 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])
total number of confs: 60
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057832 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057832/1 /scratch/stefan/7769638/working/building/REAL300000057832 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 867)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/867
`/scratch/stefan/7769638/working/3D/867' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)NN=C1C(F)(F)F)

`REAL300000057832.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057832/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057832 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)NN=C1C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 8, 14, 14, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 14, 30, 30, 30, 30, 30, 1] 30
rigid atoms, others: [0, 1, 2, 3, 35, 18, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057832 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)NN=C1C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 26, 26, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 26, 10, 7, 1, 1, 1, 1, 30] 30
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 60
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057832 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057832
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057832/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057832/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057832
Building REAL300000057833
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057833'
/scratch/stefan/7769638/working/building/REAL300000057833 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057833

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057833/0 /scratch/stefan/7769638/working/building/REAL300000057833 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 868)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/868
`/scratch/stefan/7769638/working/3D/868' -> `0.mol2'
Preparing input files

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

`REAL300000057833.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057833.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057833/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057833 none CCCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 104, 80, 23, 23, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 23, 123, 123, 123, 123, 123, 123, 123, 125, 127, 127, 127, 127, 104, 104, 80, 80, 6, 6, 1, 1, 1, 1, 123, 123, 123, 123, 123] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 17, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46])
total number of confs: 655
number of broken/clashed sets: 127
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057833 none CCCCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 46, 40, 12, 1, 12, 12, 46, 47, 47, 104, 123, 123, 119, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 46, 46, 40, 40, 46, 104, 123, 123, 123, 123, 1, 2, 2, 1, 1] 201
rigid atoms, others: [4, 42, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44])
total number of confs: 658
number of broken/clashed sets: 127
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057833 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057833
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057833/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057833
Building REAL300000057834
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057834'
/scratch/stefan/7769638/working/building/REAL300000057834 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057834

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057834/0 /scratch/stefan/7769638/working/building/REAL300000057834 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 869)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/869
`/scratch/stefan/7769638/working/3D/869' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CCC3)CC2)C=C1)

`REAL300000057834.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057834/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057834 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CCC3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 11, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1] 31
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 60
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057834 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CCC3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 30, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 32
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, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 41, 21, 22, 23, 24, 25, 26, 42])
total number of confs: 77
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057834 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057834
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057834/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057834
Building REAL300000057835
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057835'
/scratch/stefan/7769638/working/building/REAL300000057835 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057835

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057835/0 /scratch/stefan/7769638/working/building/REAL300000057835 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 870)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/870
`/scratch/stefan/7769638/working/3D/870' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1O)

`REAL300000057835.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057835.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057835/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057835 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1O 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.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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7]
1  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 1, 7, 17, 37, 37, 37, 37, 37, 1, 2] 74
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, 36])
total number of confs: 111
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057835 none CC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1O 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.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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7]
1  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 37, 22, 22, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 22, 8, 5, 1, 1, 1, 1, 37, 74] 74
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 148
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057835 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057835
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057835/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057835
Building REAL300000057836
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057836'
/scratch/stefan/7769638/working/building/REAL300000057836 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057836

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057836/0 /scratch/stefan/7769638/working/building/REAL300000057836 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 871)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/871
`/scratch/stefan/7769638/working/3D/871' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1)

`REAL300000057836.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057836/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057836 none CC(C)CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [8, 6, 8, 1, 1, 1, 1, 1, 7, 7, 28, 29, 29, 71, 81, 81, 71, 76, 81, 81, 81, 81, 1, 1, 8, 8, 8, 8, 8, 8, 8, 6, 6, 1, 7, 28, 71, 81, 81, 81, 81] 127
rigid atoms, others: [33, 3, 4, 5, 6, 7, 22, 23] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 292
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057836 none CC(C)CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [127, 127, 127, 81, 81, 81, 53, 53, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 81, 81, 127, 127, 127, 127, 127, 127, 127, 127, 127, 81, 53, 17, 7, 1, 1, 1, 1] 127
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 376
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057836 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057836
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057836/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057836
Building REAL300000057837
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057837'
/scratch/stefan/7769638/working/building/REAL300000057837 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057837

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057837/0 /scratch/stefan/7769638/working/building/REAL300000057837 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 872)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/872
`/scratch/stefan/7769638/working/3D/872' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=CC=CN=C21)

`REAL300000057837.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057837.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057837/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057837 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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]
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: [28, 28, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 51, 51, 51, 51, 51, 51, 51, 51, 51, 28, 28, 28, 16, 7, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51] 51
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 93
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057837 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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]
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, 21, 21, 21, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1] 51
rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 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])
total number of confs: 127
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057837 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057837
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057837/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057837
Building REAL300000057838
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057838'
/scratch/stefan/7769638/working/building/REAL300000057838 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057838

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057838/0 /scratch/stefan/7769638/working/building/REAL300000057838 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 873)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/873
`/scratch/stefan/7769638/working/3D/873' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=NC=CC=C2C=C1)

`REAL300000057838.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057838/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057838 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=NC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 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: [7, 7, 7, 4, 7, 6, 4, 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, 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: [28, 28, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 59, 59, 59, 59, 59, 59, 59, 59, 59, 28, 28, 28, 14, 7, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59] 59
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 105
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057838 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=NC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 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: [7, 7, 7, 4, 7, 6, 4, 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, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 35, 35, 35, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 35, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1] 59
rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 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])
total number of confs: 167
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057838 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057838
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057838/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057838
Building REAL300000057839
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057839'
/scratch/stefan/7769638/working/building/REAL300000057839 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057839

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057839/0 /scratch/stefan/7769638/working/building/REAL300000057839 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 874)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/874
`/scratch/stefan/7769638/working/3D/874' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CCCC2=CC=NC=N2)C=C1)

`REAL300000057839.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057839.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057839/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057839 none O=C([O-])C1=CC=C(NC(=O)NN=CCCC2=CC=NC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 8, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 6, 10, 10, 10, 24, 24, 118, 162, 201, 201, 201, 201, 201, 1, 1, 1, 1, 6, 10, 24, 118, 118, 162, 162, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 688
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057839 none O=C([O-])C1=CC=C(NC(=O)NN=CCCC2=CC=NC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 8, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 197, 201, 201, 197, 126, 126, 126, 78, 78, 17, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 197, 126, 78, 17, 17, 7, 7, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36])
total number of confs: 653
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057839 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057839
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057839/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057839
Building REAL300000057840
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057840'
/scratch/stefan/7769638/working/building/REAL300000057840 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057840

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057840/0 /scratch/stefan/7769638/working/building/REAL300000057840 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 875)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/875
`/scratch/stefan/7769638/working/3D/875' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057840.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057840/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057840 none C#CC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 15, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 9, 15, 26, 26, 26, 26, 26] 26
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26] set([32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057840 none C#CC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 22, 22, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 22, 12, 7, 1, 1, 1, 1] 26
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, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 52
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057840 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057840
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057840/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057840
Building REAL300000057841
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057841'
/scratch/stefan/7769638/working/building/REAL300000057841 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057841

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057841/0 /scratch/stefan/7769638/working/building/REAL300000057841 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 876)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/876
`/scratch/stefan/7769638/working/3D/876' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NSC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057841.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057841.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057841/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057841 none COC1=NSC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 8, 14, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 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, 12, 12, 12, 35, 35, 35, 59, 59, 59, 59, 59, 59, 59, 59, 59, 2, 2, 2, 1, 12, 12, 12, 35, 59, 59, 59, 59, 59] 59
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])
total number of confs: 167
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057841 none COC1=NSC=C1C(C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 8, 14, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 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, 35, 35, 35, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 35, 35, 35, 12, 7, 1, 1, 1, 1] 59
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])
total number of confs: 97
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057841 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057841
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057841/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057841
Building REAL300000057842
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057842'
/scratch/stefan/7769638/working/building/REAL300000057842 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057842

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057842/0 /scratch/stefan/7769638/working/building/REAL300000057842 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 877)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/877
`/scratch/stefan/7769638/working/3D/877' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(O)CCOCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057842.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057842/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057842 none CC(CC1(O)CCOCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 12, 5, 5, 12, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
231  conformations in input
total number of sets (complete confs): 231
using faster count positions algorithm for large data
unique positions, atoms: [22, 9, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 47, 47, 47, 76, 77, 77, 76, 77, 77, 77, 77, 77, 22, 22, 22, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 47, 76, 77, 77, 77, 77] 231
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 37, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43])
total number of confs: 253
number of broken/clashed sets: 183
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057842 none CC(CC1(O)CCOCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 12, 5, 5, 12, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
231  conformations in input
total number of sets (complete confs): 231
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 57, 77, 77, 77, 77, 77, 77, 8, 8, 7, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 26, 26, 57, 57, 231, 77, 77, 77, 77, 77, 77, 77, 77, 8, 7, 1, 1, 1, 1] 231
rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 485
number of broken/clashed sets: 183
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057842 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057842
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057842/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057842
Building REAL300000057843
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057843'
/scratch/stefan/7769638/working/building/REAL300000057843 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057843

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057843/0 /scratch/stefan/7769638/working/building/REAL300000057843 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 878)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/878
`/scratch/stefan/7769638/working/3D/878' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2COC3=C(Br)C=CC=C23)C=C1)

`REAL300000057843.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057843/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057843 none O=C([O-])C1=CC=C(NC(=O)NN=C2COC3=C(Br)C=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 8, 1, 11, 8, 8, 1, 5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 8, 10, 18, 18, 18, 18, 18, 1, 1] 18
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: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057843 none O=C([O-])C1=CC=C(NC(=O)NN=C2COC3=C(Br)C=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 8, 1, 11, 8, 8, 1, 5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 9, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 9, 1, 1, 1, 1, 1, 18, 18] 18
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33, 22, 23, 24, 25, 26, 27])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057843 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057843
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057843/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057843
Building REAL300000057844
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057844'
/scratch/stefan/7769638/working/building/REAL300000057844 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057844

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057844/0 /scratch/stefan/7769638/working/building/REAL300000057844 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 879)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/879
`/scratch/stefan/7769638/working/3D/879' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(C3CC3)=CS2)C=C1)

`REAL300000057844.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057844/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057844 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(C3CC3)=CS2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 5, 5, 5, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 14, 14, 14, 47, 47, 85, 85, 85, 121, 121, 85, 85, 1, 1, 1, 1, 9, 14, 47, 121, 121, 121, 121, 121, 85, 1, 1] 121
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 273
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057844 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(C3CC3)=CS2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 5, 5, 5, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [85, 84, 85, 84, 85, 85, 78, 33, 32, 33, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 85, 85, 85, 85, 78, 32, 8, 11, 11, 11, 11, 11, 1, 85, 85] 125
rigid atoms, others: [33, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057844 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(C3CC3)=CS2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 5, 5, 5, 1, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 125, 125, 125, 125, 124, 78, 78, 78, 42, 42, 11, 11, 11, 1, 1, 1, 1, 11, 11, 125, 125, 125, 125, 124, 78, 42, 1, 1, 1, 1, 1, 11, 125, 125] 125
rigid atoms, others: [32, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35])
total number of confs: 348
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057844 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057844
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057844/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057844
Building REAL300000057845
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057845'
/scratch/stefan/7769638/working/building/REAL300000057845 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057845

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057845/0 /scratch/stefan/7769638/working/building/REAL300000057845 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 880)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/880
`/scratch/stefan/7769638/working/3D/880' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(C)C1=CC2=CC=CC=C2S1)

`REAL300000057845.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057845/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057845 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(C)C1=CC2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 9, 9, 6, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 75, 75, 146, 146, 146, 146, 146, 146, 146, 146, 21, 21, 21, 9, 6, 1, 1, 1, 1, 75, 75, 75, 75, 146, 146, 146, 146, 146] 146
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 359
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057845 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(C)C1=CC2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [56, 12, 56, 56, 93, 93, 93, 145, 146, 146, 145, 146, 146, 146, 146, 146, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 93, 145, 146, 146, 146, 146, 12, 12, 12, 12, 1, 1, 1, 1, 1] 146
rigid atoms, others: [40, 41, 42, 43, 44, 16, 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, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 468
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057845 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057845
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057845/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057845
Building REAL300000057846
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057846'
/scratch/stefan/7769638/working/building/REAL300000057846 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057846

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057846/0 /scratch/stefan/7769638/working/building/REAL300000057846 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 881)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/881
`/scratch/stefan/7769638/working/3D/881' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(Br)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057846.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057846/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057846 none CN1C=C(Br)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 7, 7, 22, 22, 22, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 2, 2, 2, 1, 7, 22, 59, 59, 59, 59, 59] 59
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057846 none CN1C=C(Br)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 43, 43, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 59, 59, 59, 59, 59, 43, 14, 7, 1, 1, 1, 1] 59
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 111
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057846 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057846
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057846/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057846
Building REAL300000057847
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057847'
/scratch/stefan/7769638/working/building/REAL300000057847 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057847

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057847/0 /scratch/stefan/7769638/working/building/REAL300000057847 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 882)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/882
`/scratch/stefan/7769638/working/3D/882' -> `0.mol2'
Preparing input files

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

`REAL300000057847.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057847/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057847 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [44, 26, 26, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 37, 37, 26, 37, 37, 44, 44, 44, 44, 44, 13, 7, 1, 1, 1, 1, 37, 26, 37] 46
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 210
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057847 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [18, 9, 1, 9, 9, 34, 35, 35, 45, 46, 46, 45, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 34, 45, 46, 46, 46, 46, 1, 1, 1] 46
rigid atoms, others: [34, 35, 36, 2, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 170
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057847 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057847
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057847/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057847
Building REAL300000057848
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057848'
/scratch/stefan/7769638/working/building/REAL300000057848 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057848

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057848/0 /scratch/stefan/7769638/working/building/REAL300000057848 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 883)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/883
`/scratch/stefan/7769638/working/3D/883' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C)

`REAL300000057848.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057848/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057848 none COC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 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
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 8, 8, 19, 19, 19, 43, 49, 49, 45, 49, 49, 49, 49, 49, 1, 1, 1, 1, 3, 3, 3, 8, 19, 43, 49, 49, 49, 49, 1, 2, 2, 2] 49
rigid atoms, others: [1, 2, 3, 4, 33, 19, 20, 21, 22] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057848 none COC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 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
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, 39, 39, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 39, 15, 7, 1, 1, 1, 1, 49, 49, 49, 49] 49
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057848 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057848
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057848/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057848
Building REAL300000057849
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057849'
/scratch/stefan/7769638/working/building/REAL300000057849 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057849

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057849/0 /scratch/stefan/7769638/working/building/REAL300000057849 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 884)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/884
`/scratch/stefan/7769638/working/3D/884' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1)

`REAL300000057849.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057849.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057849/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057849 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 8, 1, 11, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 6, 7, 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, 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]
1  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 15, 15, 15, 32, 32, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 8, 15, 32, 124, 62, 62, 62, 62, 62, 1, 1] 124
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 235
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057849 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 8, 1, 11, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 6, 7, 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, 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]
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, 25, 25, 25, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 25, 11, 2, 1, 1, 1, 1, 1, 42, 42] 84
rigid atoms, others: [35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41])
total number of confs: 121
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057849 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057849
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057849/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057849
Building REAL300000057850
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057850'
/scratch/stefan/7769638/working/building/REAL300000057850 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057850

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057850/0 /scratch/stefan/7769638/working/building/REAL300000057850 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 885)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/885
`/scratch/stefan/7769638/working/3D/885' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1(S(C)(=O)=O)CC1)

`REAL300000057850.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057850.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057850/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057850 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 6, 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, 2, 2, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 29, 33, 33, 33, 29, 29, 19, 19, 19, 8, 6, 1, 1, 1, 1, 33, 33, 33, 29, 29, 29, 29] 33
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057850 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 6, 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, 2, 2, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 27, 29, 29, 27, 29, 29, 29, 29, 29, 1, 1, 7, 7, 7, 1, 1, 6, 6, 6, 16, 27, 29, 29, 29, 29, 7, 7, 7, 1, 1, 1, 1] 33
rigid atoms, others: [1, 35, 36, 37, 38, 16, 17, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 114
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057850 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057850
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057850/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057850
Building REAL300000057851
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057851'
/scratch/stefan/7769638/working/building/REAL300000057851 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057851

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057851/0 /scratch/stefan/7769638/working/building/REAL300000057851 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 886)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/886
`/scratch/stefan/7769638/working/3D/886' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C(CC2=CC=NC=C2)C2=CC=CC=C2)C=C1)

`REAL300000057851.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057851.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057851/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057851 none O=C([O-])C1=CC=C(NC(=O)NN=C(CC2=CC=NC=C2)C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 1, 11, 8, 8, 1, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 15, 15, 15, 34, 34, 152, 161, 161, 161, 161, 161, 34, 61, 61, 52, 61, 61, 1, 1, 1, 1, 10, 15, 152, 152, 161, 161, 161, 161, 61, 61, 52, 61, 61, 1, 1] 161
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 44, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 590
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057851 none O=C([O-])C1=CC=C(NC(=O)NN=C(CC2=CC=NC=C2)C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 1, 11, 8, 8, 1, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [166, 159, 166, 148, 166, 166, 148, 64, 64, 64, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 20, 38, 38, 30, 38, 38, 166, 166, 166, 166, 148, 64, 4, 4, 1, 1, 1, 1, 38, 38, 30, 38, 38, 166, 166] 166
rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 626
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057851 none O=C([O-])C1=CC=C(NC(=O)NN=C(CC2=CC=NC=C2)C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 1, 11, 8, 8, 1, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [63, 52, 63, 44, 63, 63, 44, 15, 15, 15, 4, 4, 1, 4, 27, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 44, 15, 27, 27, 38, 38, 38, 38, 1, 1, 1, 1, 1, 63, 63] 166
rigid atoms, others: [38, 39, 40, 41, 42, 12, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44])
total number of confs: 360
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057851 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057851
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057851/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057851
Building REAL300000057852
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057852'
/scratch/stefan/7769638/working/building/REAL300000057852 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057852

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057852/0 /scratch/stefan/7769638/working/building/REAL300000057852 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 887)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/887
`/scratch/stefan/7769638/working/3D/887' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC=C(OCCF)C=C32)C=C1)

`REAL300000057852.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057852/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057852 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC=C(OCCF)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 136, 182, 182, 50, 50, 1, 1, 1, 1, 8, 22, 50, 50, 50, 182, 182, 182, 182, 50, 1, 1] 182
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 471
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057852 none O=C([O-])C1=CC=C(NC(=O)NN=C2C(=O)NC3=CC=C(OCCF)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [50, 48, 50, 40, 50, 50, 37, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 45, 1, 1, 50, 50, 50, 50, 37, 7, 1, 1, 1, 24, 24, 45, 45, 1, 50, 50] 180
rigid atoms, others: [32, 33, 34, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 40, 41])
total number of confs: 343
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057852 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057852
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057852/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057852
Building REAL300000057853
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057853'
/scratch/stefan/7769638/working/building/REAL300000057853 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000057853

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057853/0 /scratch/stefan/7769638/working/building/REAL300000057853 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 888)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/888
`/scratch/stefan/7769638/working/3D/888' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1CC1=CC=CC=C1)

`REAL300000057853.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057853/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057853 none CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 9, 9, 9, 36, 45, 45, 36, 42, 45, 45, 45, 45, 1, 1, 1, 6, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 9, 36, 45, 45, 45, 45, 1, 1, 6, 6, 7, 7, 7, 7, 7] 50
rigid atoms, others: [0, 1, 2, 3, 4, 33, 19, 32, 42, 43, 34, 35, 20, 21, 6, 5, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 181
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057853 none CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 45, 45, 50, 50, 50, 50, 50, 50, 45, 45, 45, 45, 45, 45, 45, 45, 14, 7, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 50, 50, 50] 50
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 17, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 107
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057853 none CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CN1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 22, 50, 50, 50, 50, 50, 7, 7, 4, 4, 1, 1, 1, 1, 1] 50
rigid atoms, others: [46, 47, 48, 49, 50, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 140
number of broken/clashed sets: 48
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057853 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057853/1 /scratch/stefan/7769638/working/building/REAL300000057853 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 889)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/889
`/scratch/stefan/7769638/working/3D/889' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=C1)

`REAL300000057853.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057853/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057853 none CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 9, 23, 27, 27, 26, 26, 27, 27, 27, 27, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 9, 23, 27, 27, 27, 27, 1, 1, 5, 5, 7, 7, 7, 7, 7] 43
rigid atoms, others: [0, 1, 2, 3, 4, 33, 19, 32, 43, 44, 34, 35, 20, 21, 22, 36, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 105
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057853 none CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 9, 9, 7, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 43, 43, 43, 43, 43, 43, 27, 27, 27, 27, 27, 27, 27, 27, 9, 7, 1, 1, 1, 1, 27, 27, 43, 43, 43, 43, 43, 43, 43] 43
rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 137
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057853 none CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 43, 43, 43, 43, 43, 43, 43, 43, 43, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 24, 43, 43, 43, 43, 43, 7, 7, 3, 3, 1, 1, 1, 1, 1] 43
rigid atoms, others: [47, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 126
number of broken/clashed sets: 43
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057853 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `2'
/scratch/stefan/7769638/working/building/REAL300000057853/2 /scratch/stefan/7769638/working/building/REAL300000057853 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 2 (index: 890)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/890
`/scratch/stefan/7769638/working/3D/890' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=C1)

`REAL300000057853.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000057853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057853/2/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', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057853 none CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 9, 24, 29, 29, 24, 24, 29, 29, 29, 29, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 9, 24, 29, 29, 29, 29, 1, 1, 2, 2, 3, 3, 3, 3, 3] 29
rigid atoms, others: [0, 1, 2, 3, 4, 33, 19, 32, 43, 44, 34, 35, 20, 21, 22, 36, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 122
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057853 none CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 7, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29] 29
rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 58
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057853 none CC1CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 13, 29, 29, 29, 29, 29, 3, 3, 2, 2, 1, 1, 1, 1, 1] 29
rigid atoms, others: [47, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 87
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057853 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057853
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057853/0.*
2: /scratch/stefan/7769638/working/building/REAL300000057853/2.*
1: /scratch/stefan/7769638/working/building/REAL300000057853/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057853
Building REAL300000057854
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057854'
/scratch/stefan/7769638/working/building/REAL300000057854 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057854

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057854/0 /scratch/stefan/7769638/working/building/REAL300000057854 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 891)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/891
`/scratch/stefan/7769638/working/3D/891' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CC3)N=N2)C=C1)

`REAL300000057854.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057854/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057854 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CC3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 8, 8, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 18, 18, 18, 54, 54, 91, 91, 91, 156, 192, 192, 91, 91, 1, 1, 1, 1, 9, 18, 54, 91, 156, 156, 192, 192, 192, 192, 192, 1, 1] 192
rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057854 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CC3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 8, 8, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 74, 88, 88, 69, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 9, 32, 32, 1, 1, 88, 88, 88, 88, 69, 27, 8, 1, 9, 9, 32, 32, 32, 32, 32, 88, 88] 196
rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 382
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057854 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(CC3CC3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 8, 8, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [196, 196, 196, 196, 196, 196, 194, 138, 138, 138, 73, 73, 32, 32, 32, 8, 1, 1, 1, 1, 32, 32, 196, 196, 196, 196, 194, 138, 73, 32, 8, 8, 1, 1, 1, 1, 1, 196, 196] 196
rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38])
total number of confs: 548
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057854 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057854
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057854/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057854
Building REAL300000057855
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057855'
/scratch/stefan/7769638/working/building/REAL300000057855 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057855

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057855/0 /scratch/stefan/7769638/working/building/REAL300000057855 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 892)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/892
`/scratch/stefan/7769638/working/3D/892' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3CCOC3=C2)C=C1)

`REAL300000057855.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057855.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057855/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057855 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3CCOC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 10, 10, 24, 40, 40, 40, 40, 40, 40, 40, 1, 1] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 37, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057855 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3CCOC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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: [40, 40, 40, 40, 40, 40, 40, 24, 23, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 23, 6, 1, 1, 1, 1, 1, 1, 1, 40, 40] 40
rigid atoms, others: [32, 33, 34, 35, 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, 22, 23, 24, 25, 26, 27, 28, 37, 36])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057855 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057855
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057855/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057855
Building REAL300000057856
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057856'
/scratch/stefan/7769638/working/building/REAL300000057856 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057856

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057856/0 /scratch/stefan/7769638/working/building/REAL300000057856 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 893)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/893
`/scratch/stefan/7769638/working/3D/893' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCCC2=C1F)

`REAL300000057856.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057856.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057856/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057856 none COC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCCC2=C1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 30, 32, 32, 30, 30, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 9, 30, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1] 32
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 30, 31, 38, 39, 40, 41, 42, 43] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 32, 33, 34, 35, 36, 37])
total number of confs: 98
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057856 none COC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCCC2=C1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 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, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 13, 7, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32] 32
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43])
total number of confs: 63
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057856 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057856
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057856/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057856
Building REAL300000057857
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057857'
/scratch/stefan/7769638/working/building/REAL300000057857 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057857

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057857/0 /scratch/stefan/7769638/working/building/REAL300000057857 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 894)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/894
`/scratch/stefan/7769638/working/3D/894' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(Cl)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057857.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057857.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057857/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057857 none CN1C=C(Cl)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 9, 9, 23, 23, 23, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 2, 2, 2, 1, 9, 23, 59, 59, 59, 59, 59] 59
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057857 none CN1C=C(Cl)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 43, 43, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 59, 59, 59, 59, 59, 43, 17, 7, 1, 1, 1, 1] 59
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 116
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057857 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057857
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057857/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057857
Building REAL300000057858
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057858'
/scratch/stefan/7769638/working/building/REAL300000057858 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057858

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057858/0 /scratch/stefan/7769638/working/building/REAL300000057858 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 895)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/895
`/scratch/stefan/7769638/working/3D/895' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=C(CCCC3)N2)C=C1)

`REAL300000057858.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057858.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057858/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057858 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=C(CCCC3)N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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, 6, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 6, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1] 20
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 40
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057858 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=C(CCCC3)N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 20
rigid atoms, others: [32, 33, 34, 35, 36, 37, 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, 38, 22, 23, 24, 25, 26, 27, 28, 39])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057858 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057858
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057858/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057858
Building REAL300000057859
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057859'
/scratch/stefan/7769638/working/building/REAL300000057859 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057859

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057859/0 /scratch/stefan/7769638/working/building/REAL300000057859 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 896)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/896
`/scratch/stefan/7769638/working/3D/896' -> `0.mol2'
Preparing input files

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

`REAL300000057859.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057859.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057859/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057859 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Cl)=NC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 16, 1, 1, 7, 7, 6, 6, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 10, 10, 10, 22, 22, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 8, 10, 22, 28, 28, 1, 1] 28
rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057859 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(Cl)=NC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 16, 1, 1, 7, 7, 6, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 16, 8, 1, 1, 29, 29] 29
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 81
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057859 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057859
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057859/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057859
Building REAL300000057860
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057860'
/scratch/stefan/7769638/working/building/REAL300000057860 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057860

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057860/0 /scratch/stefan/7769638/working/building/REAL300000057860 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 897)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/897
`/scratch/stefan/7769638/working/3D/897' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2NC(C)=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1)

`REAL300000057860.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057860.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057860/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057860 none COC1=CC=C2NC(C)=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 35, 65, 81, 81, 65, 65, 81, 81, 81, 81, 1, 1, 3, 3, 3, 1, 1, 1, 2, 2, 2, 12, 34, 65, 81, 81, 81, 81, 1] 81
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 43, 25, 26, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 313
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057860 none COC1=CC=C2NC(C)=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 81, 81, 24, 24, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 24, 6, 6, 1, 1, 1, 1, 81] 81
rigid atoms, others: [39, 40, 41, 42, 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, 36, 37, 38, 43])
total number of confs: 108
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057860 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057860
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057860/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057860
Building REAL300000057861
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057861'
/scratch/stefan/7769638/working/building/REAL300000057861 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057861

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057861/0 /scratch/stefan/7769638/working/building/REAL300000057861 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 898)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/898
`/scratch/stefan/7769638/working/3D/898' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CC2)=NN1C)

`REAL300000057861.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057861/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057861 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [41, 41, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 94, 94, 94, 122, 122, 94, 94, 94, 41, 41, 41, 17, 7, 1, 1, 1, 1, 94, 122, 122, 122, 122, 122, 94, 94, 94] 122
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 264
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057861 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 1, 10, 10, 33, 33, 33, 81, 94, 94, 81, 88, 94, 94, 94, 94, 1, 1, 1, 1, 13, 13, 1, 1, 1, 10, 10, 10, 33, 81, 94, 94, 94, 94, 1, 13, 13, 13, 13, 13, 2, 2, 2] 122
rigid atoms, others: [1, 34, 16, 17, 18, 19, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 354
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057861 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [54, 13, 54, 54, 89, 89, 89, 122, 122, 122, 122, 122, 122, 122, 122, 122, 13, 13, 1, 1, 1, 1, 13, 13, 13, 54, 54, 54, 89, 122, 122, 122, 122, 122, 13, 1, 1, 1, 1, 1, 13, 13, 13] 122
rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 336
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057861 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057861
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057861/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057861
Building REAL300000057862
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057862'
/scratch/stefan/7769638/working/building/REAL300000057862 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057862

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057862/0 /scratch/stefan/7769638/working/building/REAL300000057862 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 899)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/899
`/scratch/stefan/7769638/working/3D/899' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCC2)=NN1C)

`REAL300000057862.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057862.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057862/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057862 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [40, 40, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 94, 94, 94, 150, 150, 150, 94, 94, 94, 40, 40, 40, 17, 7, 1, 1, 1, 1, 94, 150, 150, 150, 150, 150, 150, 150, 94, 94, 94] 150
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 341
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057862 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 1, 10, 10, 33, 33, 33, 83, 94, 94, 89, 94, 94, 94, 94, 94, 1, 1, 1, 1, 13, 13, 13, 1, 1, 1, 10, 10, 10, 33, 83, 94, 94, 94, 94, 1, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2] 150
rigid atoms, others: [1, 35, 16, 17, 18, 19, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 305
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057862 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [59, 13, 59, 59, 95, 95, 95, 146, 150, 150, 150, 150, 150, 150, 150, 150, 13, 13, 1, 1, 1, 1, 1, 13, 13, 13, 59, 59, 59, 95, 146, 150, 150, 150, 150, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 150
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45])
total number of confs: 410
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057862 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057862
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057862/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057862
Building REAL300000057863
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057863'
/scratch/stefan/7769638/working/building/REAL300000057863 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057863

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057863/0 /scratch/stefan/7769638/working/building/REAL300000057863 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 900)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/900
`/scratch/stefan/7769638/working/3D/900' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2C3CCCCC23)C=C1)

`REAL300000057863.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057863/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057863 none O=C([O-])C1=CC=C(NC(=O)NN=CC2C3CCCCC23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 17, 17, 17, 25, 25, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 11, 17, 25, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1] 72
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 187
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057863 none O=C([O-])C1=CC=C(NC(=O)NN=CC2C3CCCCC23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 29, 29, 29, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 29, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72] 72
rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 38, 39])
total number of confs: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057863 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057863
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057863/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057863
Building REAL300000057864
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057864'
/scratch/stefan/7769638/working/building/REAL300000057864 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057864

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057864/0 /scratch/stefan/7769638/working/building/REAL300000057864 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 901)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/901
`/scratch/stefan/7769638/working/3D/901' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CS1)

`REAL300000057864.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057864/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057864 none CS(=O)(=O)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [8, 1, 8, 8, 1, 1, 1, 4, 4, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 8, 8, 8, 4, 7, 13, 13, 13, 13, 13, 1, 1] 19
rigid atoms, others: [1, 34, 35, 4, 5, 6, 21, 22, 23] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057864 none CS(=O)(=O)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 13, 19, 19, 13, 8, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 19, 19, 19, 8, 6, 6, 1, 1, 1, 1, 13, 13] 19
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, 34, 35])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057864 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057864
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057864/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057864
Building REAL300000057865
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057865'
/scratch/stefan/7769638/working/building/REAL300000057865 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057865

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057865/0 /scratch/stefan/7769638/working/building/REAL300000057865 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 902)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/902
`/scratch/stefan/7769638/working/3D/902' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3COCCC3=C2)C=C1)

`REAL300000057865.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057865.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057865/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057865 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3COCCC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 12, 12, 12, 28, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 8, 12, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1] 45
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057865 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C3COCCC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 21, 20, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 45
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 23, 24, 25, 26, 27, 28, 29, 39])
total number of confs: 121
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057865 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057865
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057865/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057865
Building REAL300000057866
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057866'
/scratch/stefan/7769638/working/building/REAL300000057866 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057866

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057866/0 /scratch/stefan/7769638/working/building/REAL300000057866 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 903)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/903
`/scratch/stefan/7769638/working/3D/903' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=C1OC=C2)

`REAL300000057866.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057866.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057866/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057866 none CC1(C)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=C1OC=C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 7, 7, 18, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 19, 19, 19, 19, 1, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42] set([35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40])
total number of confs: 43
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057866 none CC1(C)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C2=C1OC=C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 16, 7, 1, 1, 1, 1, 19, 19] 19
rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 53
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057866 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057866
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057866/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057866
Building REAL300000057867
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057867'
/scratch/stefan/7769638/working/building/REAL300000057867 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057867

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057867/0 /scratch/stefan/7769638/working/building/REAL300000057867 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 904)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/904
`/scratch/stefan/7769638/working/3D/904' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)SC(Cl)=C1)

`REAL300000057867.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057867.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057867/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057867 none O=C([O-])C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 16, 1, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 1] 3
rigid atoms, others: [1, 3, 4, 5, 20, 21, 22, 23, 31] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 13
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057867 none O=C([O-])C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 16, 1, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3] 3
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 11
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057867 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057867
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057867/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057867
Building REAL300000057868
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057868'
/scratch/stefan/7769638/working/building/REAL300000057868 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057868

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057868/0 /scratch/stefan/7769638/working/building/REAL300000057868 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 905)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/905
`/scratch/stefan/7769638/working/3D/905' -> `0.mol2'
Preparing input files

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

`REAL300000057868.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057868/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057868 none O=C([O-])C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 1, 1] 3
rigid atoms, others: [1, 3, 4, 5, 20, 21, 22, 30, 31] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 13
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057868 none O=C([O-])C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 3
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 11
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057868 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057868
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057868/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057868
Building REAL300000057869
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057869'
/scratch/stefan/7769638/working/building/REAL300000057869 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057869

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057869/0 /scratch/stefan/7769638/working/building/REAL300000057869 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 906)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/906
`/scratch/stefan/7769638/working/3D/906' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057869.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057869.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057869/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057869 none CC1=CC=CC(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 37, 37, 80, 80, 80, 80, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 1, 12, 37, 80, 80, 80, 80, 80] 80
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28] set([9, 10, 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: 227
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057869 none CC1=CC=CC(F)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 80, 80, 80, 80, 80, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 80, 80, 80, 80, 80, 80, 34, 16, 7, 1, 1, 1, 1] 80
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: 139
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057869 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057869
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057869/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057869
Building REAL300000057870
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057870'
/scratch/stefan/7769638/working/building/REAL300000057870 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057870

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057870/0 /scratch/stefan/7769638/working/building/REAL300000057870 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 907)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/907
`/scratch/stefan/7769638/working/3D/907' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2C2CCC2)C=C1)

`REAL300000057870.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057870/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057870 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 41, 41, 83, 83, 70, 83, 83, 83, 105, 105, 105, 1, 1, 1, 1, 10, 16, 41, 83, 83, 73, 83, 105, 105, 105, 105, 105, 105, 105, 1, 1] 105
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 266
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057870 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [72, 70, 72, 68, 72, 72, 68, 33, 33, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 72, 72, 72, 72, 68, 33, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 72, 72] 91
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 220
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057870 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 91, 91, 91, 91, 91, 49, 49, 49, 22, 22, 5, 5, 5, 4, 5, 5, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 49, 22, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 91, 91] 91
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42])
total number of confs: 257
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057870 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057870
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057870/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057870
Building REAL300000057871
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057871'
/scratch/stefan/7769638/working/building/REAL300000057871 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057871

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057871/0 /scratch/stefan/7769638/working/building/REAL300000057871 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 908)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/908
`/scratch/stefan/7769638/working/3D/908' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CCOCC2)=N1)

`REAL300000057871.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057871/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057871 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CCOCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 7, 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, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 42, 42, 42, 110, 115, 115, 115, 115, 115, 115, 115, 115, 1, 1, 7, 7, 7, 7, 7, 1, 2, 2, 2, 1, 12, 41, 110, 115, 115, 115, 115, 7, 7, 7, 7, 7, 7, 7, 7, 7] 180
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 324
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057871 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CCOCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 7, 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, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [115, 115, 115, 44, 44, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 115, 115, 180, 180, 180, 180, 180, 115, 115, 115, 115, 115, 44, 14, 7, 1, 1, 1, 1, 180, 180, 180, 180, 180, 180, 180, 180, 180] 180
rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 426
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057871 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2CCOCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 7, 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, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 36, 36, 79, 79, 79, 176, 180, 180, 180, 180, 180, 180, 180, 180, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 36, 79, 176, 180, 180, 180, 180, 1, 1, 1, 1, 1, 1, 1, 1, 1] 180
rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 492
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057871 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057871
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057871/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057871
Building REAL300000057872
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057872'
/scratch/stefan/7769638/working/building/REAL300000057872 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057872

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057872/0 /scratch/stefan/7769638/working/building/REAL300000057872 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 909)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/909
`/scratch/stefan/7769638/working/3D/909' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=CC(C3=CC=CN=C3)=C2)C=C1)

`REAL300000057872.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057872.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057872/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057872 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=CC(C3=CC=CN=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 33, 33, 33, 33, 33, 18, 1, 1, 1, 1, 5, 6, 6, 18, 18, 33, 33, 33, 33, 18, 1, 1] 33
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 25, 26, 27, 28] set([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: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057872 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=CC(C3=CC=CN=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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]
0  hydrogens 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, 111, 133, 104, 133, 133, 104, 41, 40, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 133, 133, 133, 133, 104, 40, 11, 1, 1, 5, 5, 5, 5, 1, 133, 133] 201
rigid atoms, others: [32, 33, 38, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 39, 40])
total number of confs: 513
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057872 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN=CC(C3=CC=CN=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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]
0  hydrogens need rotated
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, 201, 201, 200, 107, 107, 107, 35, 35, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 201, 201, 201, 201, 200, 107, 35, 5, 5, 1, 1, 1, 1, 5, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40])
total number of confs: 561
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057872 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057872
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057872/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057872
Building REAL300000057873
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057873'
/scratch/stefan/7769638/working/building/REAL300000057873 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057873

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057873/0 /scratch/stefan/7769638/working/building/REAL300000057873 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 910)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/910
`/scratch/stefan/7769638/working/3D/910' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1C(C)(C)C)

`REAL300000057873.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057873.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057873/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057873 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [7, 7, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 5, 5, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 9
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 19
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057873 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 7, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 9
rigid atoms, others: [1, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 33
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057873 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057873
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057873/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057873
Building REAL300000057874
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057874'
/scratch/stefan/7769638/working/building/REAL300000057874 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057874

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057874/0 /scratch/stefan/7769638/working/building/REAL300000057874 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 911)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/911
`/scratch/stefan/7769638/working/3D/911' -> `0.mol2'
Preparing input files

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

`REAL300000057874.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057874.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057874/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057874 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [33, 33, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 33, 59, 59, 59, 59, 59, 59, 33, 33, 33, 15, 7, 1, 1, 1, 1, 59, 59, 59, 118] 118
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 232
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057874 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [9, 1, 9, 9, 33, 34, 34, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 33, 59, 59, 59, 59, 59, 1, 1, 1, 2] 118
rigid atoms, others: [32, 1, 34, 33, 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, 35])
total number of confs: 169
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057874 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057874
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057874/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057874
Building REAL300000057875
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057875'
/scratch/stefan/7769638/working/building/REAL300000057875 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057875

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057875/0 /scratch/stefan/7769638/working/building/REAL300000057875 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 912)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/912
`/scratch/stefan/7769638/working/3D/912' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC(C)=CN1)

`REAL300000057875.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057875.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057875/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057875 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC(C)=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 5, 1, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 7, 1, 1, 1, 1, 13, 13, 13, 13, 13] 13
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35])
total number of confs: 37
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057875 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NC(C)=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 5, 1, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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, 8, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1] 13
rigid atoms, others: [1, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 45
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057875 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057875
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057875/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057875
Building REAL300000057876
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057876'
/scratch/stefan/7769638/working/building/REAL300000057876 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057876

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057876/0 /scratch/stefan/7769638/working/building/REAL300000057876 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 913)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/913
`/scratch/stefan/7769638/working/3D/913' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC(COCC3=CC=CC=C3)C2)C=C1)

`REAL300000057876.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057876.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057876/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057876 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(COCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 5, 9, 9, 9, 9, 45, 109, 201, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 5, 5, 9, 9, 9, 45, 45, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 46, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 689
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057876 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(COCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 8, 4, 3, 4, 1, 1, 1, 1, 1, 1, 9, 33, 90, 140, 140, 98, 140, 140, 1, 9, 9, 9, 9, 8, 3, 1, 1, 1, 9, 9, 90, 90, 140, 140, 140, 140, 140, 1, 1, 9, 9] 201
rigid atoms, others: [32, 33, 43, 44, 10, 11, 12, 13, 14, 15, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057876 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(COCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 172, 172, 172, 140, 140, 140, 140, 56, 14, 3, 1, 1, 1, 1, 1, 1, 1, 140, 201, 201, 201, 201, 201, 172, 140, 140, 140, 56, 56, 3, 3, 1, 1, 1, 1, 1, 140, 140, 201, 201] 201
rigid atoms, others: [38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46])
total number of confs: 673
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057876 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057876
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057876/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057876
Building REAL300000057877
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057877'
/scratch/stefan/7769638/working/building/REAL300000057877 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057877

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057877/0 /scratch/stefan/7769638/working/building/REAL300000057877 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 914)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/914
`/scratch/stefan/7769638/working/3D/914' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1)

`REAL300000057877.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057877.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057877/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057877 none CSC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 37, 37, 37, 102, 114, 114, 102, 106, 114, 114, 114, 114, 1, 12, 12, 12, 1, 1, 1, 11, 37, 102, 114, 114, 114, 114, 1] 153
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22, 36, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 383
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057877 none CSC1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [153, 114, 114, 114, 114, 114, 41, 41, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 114, 153, 153, 153, 114, 114, 114, 41, 14, 7, 1, 1, 1, 1, 114] 153
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: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057877 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057877
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057877/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057877
Building REAL300000057878
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057878'
/scratch/stefan/7769638/working/building/REAL300000057878 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057878

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057878/0 /scratch/stefan/7769638/working/building/REAL300000057878 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 915)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/915
`/scratch/stefan/7769638/working/3D/915' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)N1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057878.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057878.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057878/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057878 none CC(C)(C)N1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 3, 3, 7, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 3, 7, 16, 16, 16, 16, 16] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33, 27, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057878 none CC(C)(C)N1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 12, 12, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 4, 4, 1, 1, 1, 1] 16
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 25
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057878 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057878
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057878/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057878
Building REAL300000057879
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057879'
/scratch/stefan/7769638/working/building/REAL300000057879 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057879

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057879/0 /scratch/stefan/7769638/working/building/REAL300000057879 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 916)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/916
`/scratch/stefan/7769638/working/3D/916' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC(Cl)=CC=C3C2)C=C1)

`REAL300000057879.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057879.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057879/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057879 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC(Cl)=CC=C3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 8, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1] 30
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 63
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057879 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3=CC(Cl)=CC=C3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 30, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 31
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 23, 24, 25, 26, 27, 28])
total number of confs: 77
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057879 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057879
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057879/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057879
Building REAL300000057880
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057880'
/scratch/stefan/7769638/working/building/REAL300000057880 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057880

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057880/0 /scratch/stefan/7769638/working/building/REAL300000057880 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 917)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/917
`/scratch/stefan/7769638/working/3D/917' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=C(CCCCC3)S2)C=C1)

`REAL300000057880.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057880.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057880/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057880 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=C(CCCCC3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 5, 5, 5, 5, 5, 14, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 5
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 41, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 13
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057880 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=C(CCCCC3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 5, 5, 5, 5, 5, 14, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 42, 42, 42, 42, 18, 17, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42] 42
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 41, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 119
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057880 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057880
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057880/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057880
Building REAL300000057881
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057881'
/scratch/stefan/7769638/working/building/REAL300000057881 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057881

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057881/0 /scratch/stefan/7769638/working/building/REAL300000057881 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 918)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/918
`/scratch/stefan/7769638/working/3D/918' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=CC=C3C=C2O)C=C1)

`REAL300000057881.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057881.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057881/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057881 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=CC=C3C=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 10, 1, 1] 10
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 29
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057881 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=CC=C3C=C2O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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, 13, 13, 13, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 13, 9, 1, 1, 1, 1, 1, 1, 2, 23, 23] 46
rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 65
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057881 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057881
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057881/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057881
Building REAL300000057882
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057882'
/scratch/stefan/7769638/working/building/REAL300000057882 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057882

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057882/0 /scratch/stefan/7769638/working/building/REAL300000057882 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 919)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/919
`/scratch/stefan/7769638/working/3D/919' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C2CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CC21)

`REAL300000057882.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057882/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057882 none CC1(C)C2CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 10, 10, 24, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 9, 24, 25, 25, 25, 25, 1, 1, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 20, 21, 38, 28, 29, 30, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 75
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057882 none CC1(C)C2CC(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 7, 1, 1, 1, 1, 25, 25, 25] 25
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39])
total number of confs: 57
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057882 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057882
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057882/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057882
Building REAL300000057883
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057883'
/scratch/stefan/7769638/working/building/REAL300000057883 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057883

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057883/0 /scratch/stefan/7769638/working/building/REAL300000057883 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 920)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/920
`/scratch/stefan/7769638/working/3D/920' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=NC=CS1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057883.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057883/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057883 none CC(CCC1=NC=CS1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 8, 1, 1, 14, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [23, 9, 3, 1, 1, 1, 1, 1, 1, 23, 23, 41, 41, 41, 99, 99, 99, 99, 99, 99, 99, 99, 99, 23, 23, 23, 9, 9, 3, 3, 1, 1, 41, 99, 99, 99, 99, 99] 99
rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37])
total number of confs: 311
number of broken/clashed sets: 95
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057883 none CC(CCC1=NC=CS1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 8, 1, 1, 14, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [15, 15, 15, 61, 61, 99, 99, 99, 99, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 61, 61, 61, 61, 99, 99, 5, 3, 1, 1, 1, 1] 99
rigid atoms, others: [34, 35, 36, 37, 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])
total number of confs: 261
number of broken/clashed sets: 95
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057883 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057883
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057883/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057883
Building REAL300000057884
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057884'
/scratch/stefan/7769638/working/building/REAL300000057884 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057884

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057884/0 /scratch/stefan/7769638/working/building/REAL300000057884 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 921)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/921
`/scratch/stefan/7769638/working/3D/921' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=NS1)

`REAL300000057884.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057884.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057884/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057884 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'N.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 8, 14, 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, 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: [20, 20, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 30, 30, 30, 30, 30, 20, 20, 20, 10, 7, 1, 1, 1, 1, 30, 30, 30, 30] 30
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 60
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057884 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'N.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 8, 14, 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, 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: [10, 1, 10, 10, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 11, 11, 11, 20, 30, 30, 30, 30, 30, 1, 2, 2, 2] 30
rigid atoms, others: [1, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34])
total number of confs: 90
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057884 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057884
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057884/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057884
Building REAL300000057885
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057885'
/scratch/stefan/7769638/working/building/REAL300000057885 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057885

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057885/0 /scratch/stefan/7769638/working/building/REAL300000057885 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 922)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/922
`/scratch/stefan/7769638/working/3D/922' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC(C2)O3)C=C1)

`REAL300000057885.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057885.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057885/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057885 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC(C2)O3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 12, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 36, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 54
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057885 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCC(C2)O3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 23
rigid atoms, others: [32, 33, 34, 35, 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, 8, 9, 20, 21, 22, 23, 24, 25, 37, 36])
total number of confs: 59
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057885 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057885
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057885/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057885
Building REAL300000057886
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057886'
/scratch/stefan/7769638/working/building/REAL300000057886 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057886

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057886/0 /scratch/stefan/7769638/working/building/REAL300000057886 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 923)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/923
`/scratch/stefan/7769638/working/3D/923' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3C(C2)C3(F)F)C=C1)

`REAL300000057886.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057886.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057886/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057886 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3C(C2)C3(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 9, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 9, 11, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 46
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057886 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3C(C2)C3(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 22, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 23
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 22, 23, 24, 25, 26, 36])
total number of confs: 55
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057886 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057886
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057886/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057886
Building REAL300000057887
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057887'
/scratch/stefan/7769638/working/building/REAL300000057887 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057887

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057887/0 /scratch/stefan/7769638/working/building/REAL300000057887 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 924)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/924
`/scratch/stefan/7769638/working/3D/924' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CS1)

`REAL300000057887.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057887.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057887/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057887 none O=C([O-])C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 6, 6, 15, 16, 16, 49, 50, 50, 49, 49, 50, 50, 50, 50, 1, 1, 1, 6, 15, 49, 50, 50, 50, 50, 1] 50
rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 146
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057887 none O=C([O-])C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 50, 41, 41, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 50, 50, 50, 41, 16, 7, 1, 1, 1, 1, 50] 50
rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057887 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057887
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057887/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057887
Building REAL300000057888
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057888'
/scratch/stefan/7769638/working/building/REAL300000057888 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057888

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057888/0 /scratch/stefan/7769638/working/building/REAL300000057888 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 925)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/925
`/scratch/stefan/7769638/working/3D/925' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CC3(F)F)N=C2)C=C1)

`REAL300000057888.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057888.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057888/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057888 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CC3(F)F)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 15, 15, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 10, 18, 18, 18, 54, 54, 102, 102, 102, 201, 201, 201, 201, 102, 102, 1, 1, 1, 1, 10, 18, 54, 102, 201, 201, 201, 102, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 23, 24, 25, 26, 36] set([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: 456
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057888 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CC3(F)F)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 15, 15, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [105, 101, 105, 96, 105, 105, 92, 34, 34, 34, 8, 8, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 105, 105, 105, 105, 92, 33, 8, 1, 12, 12, 12, 1, 105, 105] 194
rigid atoms, others: [34, 12, 13, 14, 15, 16, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36])
total number of confs: 341
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057888 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CC3(F)F)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 15, 15, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [194, 194, 194, 190, 194, 194, 190, 122, 122, 122, 61, 61, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 194, 194, 194, 194, 190, 122, 61, 12, 1, 1, 1, 12, 194, 194] 194
rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 579
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057888 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057888
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057888/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057888
Building REAL300000057889
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057889'
/scratch/stefan/7769638/working/building/REAL300000057889 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057889

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057889/0 /scratch/stefan/7769638/working/building/REAL300000057889 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 926)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/926
`/scratch/stefan/7769638/working/3D/926' -> `0.mol2'
Preparing input files

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

`REAL300000057889.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057889.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057889/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057889 none CC(C)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 12, 12, 26, 27, 27, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 3, 3, 3, 2, 3, 3, 3, 12, 26, 51, 51, 51, 51, 51, 2, 2, 2, 1] 51
rigid atoms, others: [1, 3, 4, 5, 41, 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, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 167
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057889 none CC(C)C1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)N(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 28, 28, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 28, 14, 7, 1, 1, 1, 1, 51, 51, 51, 51] 51
rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 91
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057889 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057889
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057889/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057889
Building REAL300000057890
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057890'
/scratch/stefan/7769638/working/building/REAL300000057890 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057890

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057890/0 /scratch/stefan/7769638/working/building/REAL300000057890 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 927)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/927
`/scratch/stefan/7769638/working/3D/927' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2C=C1)

`REAL300000057890.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057890.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057890/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057890 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 67, 67, 67, 67, 67, 67, 67, 67, 67, 30, 30, 30, 16, 7, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67] 67
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 116
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057890 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 33, 33, 33, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 33, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1] 67
rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 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])
total number of confs: 183
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057890 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057890
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057890/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057890
Building REAL300000057891
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057891'
/scratch/stefan/7769638/working/building/REAL300000057891 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057891

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057891/0 /scratch/stefan/7769638/working/building/REAL300000057891 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 928)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/928
`/scratch/stefan/7769638/working/3D/928' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000057891.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057891.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057891/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057891 none COCC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [21, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 60, 60, 60, 134, 149, 149, 142, 149, 149, 149, 149, 149, 1, 1, 21, 21, 21, 5, 5, 1, 1, 13, 13, 13, 60, 134, 149, 149, 149, 149, 1, 1] 189
rigid atoms, others: [2, 3, 4, 5, 6, 7, 41, 42, 23, 24, 30, 31] set([0, 1, 8, 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])
total number of confs: 458
number of broken/clashed sets: 125
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057891 none COCC1=CC=C(C(C)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [189, 179, 52, 52, 149, 149, 52, 52, 52, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 149, 149, 189, 189, 189, 179, 179, 149, 149, 52, 52, 52, 16, 7, 1, 1, 1, 1, 149, 149] 189
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 927
number of broken/clashed sets: 125
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057891 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057891
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057891/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057891
Building REAL300000057892
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057892'
/scratch/stefan/7769638/working/building/REAL300000057892 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057892

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057892/0 /scratch/stefan/7769638/working/building/REAL300000057892 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 929)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/929
`/scratch/stefan/7769638/working/3D/929' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=CC2=C1CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057892.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057892.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057892/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057892 none N#CC1=CC=CC2=C1CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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: [8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 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, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 18] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 47
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057892 none N#CC1=CC=CC2=C1CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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: [8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 18, 18, 18, 18, 13, 7, 1, 1, 1, 1] 18
rigid atoms, others: [34, 35, 36, 37, 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])
total number of confs: 51
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057892 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057892
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057892/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057892
Building REAL300000057893
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057893'
/scratch/stefan/7769638/working/building/REAL300000057893 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057893

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057893/0 /scratch/stefan/7769638/working/building/REAL300000057893 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 930)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/930
`/scratch/stefan/7769638/working/3D/930' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C)=N1)

`REAL300000057893.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057893.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057893/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057893 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 6, 6, 16, 17, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 2, 2, 2, 1, 6, 16, 26, 26, 26, 26, 26, 1, 2, 2, 2] 26
rigid atoms, others: [0, 1, 2, 3, 4, 34, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057893 none CC1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
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, 24, 24, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 24, 26, 26, 26, 26, 24, 12, 7, 1, 1, 1, 1, 26, 26, 26, 26] 26
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: 58
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057893 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057893
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057893/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057893
Building REAL300000057894
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057894'
/scratch/stefan/7769638/working/building/REAL300000057894 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057894

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057894/0 /scratch/stefan/7769638/working/building/REAL300000057894 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 931)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/931
`/scratch/stefan/7769638/working/3D/931' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Br)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)S1)

`REAL300000057894.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057894.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057894/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057894 none CC1=C(Br)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 14, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 12, 12, 30, 30, 30, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 2, 2, 2, 12, 30, 61, 61, 61, 61, 61, 2, 2, 2] 61
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 187
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057894 none CC1=C(Br)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 14, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 61, 33, 33, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 33, 16, 7, 1, 1, 1, 1, 61, 61, 61] 61
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 109
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057894 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057894
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057894/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057894
Building REAL300000057895
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057895'
/scratch/stefan/7769638/working/building/REAL300000057895 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057895

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057895/0 /scratch/stefan/7769638/working/building/REAL300000057895 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 932)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/932
`/scratch/stefan/7769638/working/3D/932' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CC3)C3=CC=CC=C32)C=C1)

`REAL300000057895.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057895.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057895/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057895 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CC3)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 10, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 43, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 55
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057895 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCC3(CC3)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 11, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 25
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 43, 24, 25, 26, 27, 28, 29])
total number of confs: 65
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057895 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057895
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057895/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057895
Building REAL300000057896
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057896'
/scratch/stefan/7769638/working/building/REAL300000057896 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057896

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057896/0 /scratch/stefan/7769638/working/building/REAL300000057896 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 933)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/933
`/scratch/stefan/7769638/working/3D/933' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC(F)=C2)=N1)

`REAL300000057896.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057896.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057896/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057896 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC(F)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 36, 36, 36, 84, 95, 95, 84, 88, 95, 95, 95, 95, 1, 1, 11, 11, 10, 11, 11, 11, 1, 2, 2, 2, 1, 13, 36, 84, 95, 95, 95, 95, 11, 11, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 340
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057896 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC(F)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 35, 35, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 95, 95, 201, 201, 201, 201, 201, 201, 95, 95, 95, 95, 95, 35, 10, 7, 1, 1, 1, 1, 201, 201, 201, 201] 201
rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 307
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057896 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC(F)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 11, 44, 44, 94, 94, 94, 199, 201, 201, 199, 200, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 44, 94, 199, 201, 201, 201, 201, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 588
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057896 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057896
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057896/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057896
Building REAL300000057897
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057897'
/scratch/stefan/7769638/working/building/REAL300000057897 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057897

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057897/0 /scratch/stefan/7769638/working/building/REAL300000057897 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 934)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/934
`/scratch/stefan/7769638/working/3D/934' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=N1)

`REAL300000057897.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057897.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057897/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057897 none CCCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 10, 10, 36, 36, 36, 77, 97, 97, 85, 85, 97, 97, 97, 97, 1, 1, 1, 17, 17, 17, 17, 17, 9, 9, 1, 10, 36, 77, 97, 97, 97, 97, 2, 2, 2] 201
rigid atoms, others: [2, 3, 4, 5, 6, 21, 22, 23, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 414
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057897 none CCCN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 97, 97, 97, 37, 37, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 201, 201, 201, 201, 201, 201, 201, 97, 37, 12, 7, 1, 1, 1, 1, 97, 97, 97] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41])
total number of confs: 644
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057897 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057897
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057897/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057897
Building REAL300000057898
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057898'
/scratch/stefan/7769638/working/building/REAL300000057898 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057898

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057898/0 /scratch/stefan/7769638/working/building/REAL300000057898 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 935)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/935
`/scratch/stefan/7769638/working/3D/935' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057898.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057898.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057898/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057898 none CCN1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [8, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 39, 41, 41, 40, 40, 41, 41, 41, 41, 1, 8, 8, 8, 8, 8, 1, 1, 7, 17, 39, 41, 41, 41, 41] 65
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 134
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057898 none CCN1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 41, 41, 41, 41, 34, 34, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 41, 65, 65, 65, 65, 65, 41, 41, 34, 16, 7, 1, 1, 1, 1] 65
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 230
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057898 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057898
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057898/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057898
Building REAL300000057899
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057899'
/scratch/stefan/7769638/working/building/REAL300000057899 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057899

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057899/0 /scratch/stefan/7769638/working/building/REAL300000057899 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 936)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/936
`/scratch/stefan/7769638/working/3D/936' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(C)CC1=CC=CC=C1)

`REAL300000057899.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057899.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057899/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057899 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(C)CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [61, 40, 40, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 69, 69, 90, 90, 90, 90, 90, 90, 61, 61, 61, 61, 61, 16, 7, 1, 1, 1, 1, 69, 69, 69, 69, 90, 90, 90, 90, 90, 90, 90] 112
rigid atoms, others: [33, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 438
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057899 none CCC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(C)CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [38, 20, 6, 20, 20, 45, 45, 45, 88, 90, 90, 88, 88, 90, 90, 90, 90, 2, 6, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 45, 88, 90, 90, 90, 90, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1] 112
rigid atoms, others: [43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 377
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057899 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057899
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057899/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057899
Building REAL300000057900
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057900'
/scratch/stefan/7769638/working/building/REAL300000057900 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057900

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057900/0 /scratch/stefan/7769638/working/building/REAL300000057900 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 937)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/937
`/scratch/stefan/7769638/working/3D/937' -> `0.mol2'
Preparing input files

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

`REAL300000057900.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057900.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057900/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057900 none CC(C)C1=CC(O)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 43, 44, 44, 96, 99, 99, 98, 99, 99, 99, 99, 99, 1, 4, 4, 4, 4, 4, 4, 4, 1, 2, 1, 11, 43, 96, 99, 99, 99, 99, 1] 210
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 42, 24] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 276
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057900 none CC(C)C1=CC(O)=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [105, 99, 105, 99, 99, 99, 99, 99, 47, 47, 19, 19, 7, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 99, 105, 105, 105, 105, 105, 105, 105, 99, 198, 99, 47, 19, 7, 1, 1, 1, 1, 99] 210
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 401
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057900 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057900
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057900/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057900
Building REAL300000057901
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057901'
/scratch/stefan/7769638/working/building/REAL300000057901 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057901

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057901/0 /scratch/stefan/7769638/working/building/REAL300000057901 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 938)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/938
`/scratch/stefan/7769638/working/3D/938' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=NC=CC=C3O2)C=C1)

`REAL300000057901.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057901/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057901 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=NC=CC=C3O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 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, 3, 7, 7, 7, 7, 3, 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, 8, 10, 10, 10, 26, 26, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 8, 10, 26, 39, 39, 39, 39, 1, 1] 39
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 22, 23, 24, 25, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 72
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057901 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=NC=CC=C3O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 6, 7, 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, 3, 7, 7, 7, 7, 3, 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, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 14, 6, 1, 1, 1, 1, 39, 39] 39
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, 34, 33, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 106
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057901 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057901
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057901/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057901
Building REAL300000057902
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057902'
/scratch/stefan/7769638/working/building/REAL300000057902 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057902

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057902/0 /scratch/stefan/7769638/working/building/REAL300000057902 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 939)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/939
`/scratch/stefan/7769638/working/3D/939' -> `0.mol2'
Preparing input files

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

`REAL300000057902.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057902.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057902/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057902 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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]
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: [26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 53, 53, 47, 53, 53, 53, 26, 26, 26, 14, 7, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53] 53
rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37])
total number of confs: 121
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057902 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=NC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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]
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, 31, 31, 31, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 31, 53, 53, 53, 53, 53, 1, 1, 1, 2, 2, 2] 53
rigid atoms, others: [32, 1, 34, 33, 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, 35, 36, 37])
total number of confs: 149
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057902 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057902
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057902/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057902
Building REAL300000057903
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057903'
/scratch/stefan/7769638/working/building/REAL300000057903 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057903

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057903/0 /scratch/stefan/7769638/working/building/REAL300000057903 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 940)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/940
`/scratch/stefan/7769638/working/3D/940' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)OC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057903.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057903.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057903/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057903 none CC1=C(C)OC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 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
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, 6, 6, 14, 15, 15, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 2, 2, 2, 6, 14, 41, 41, 41, 41, 41] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21] set([7, 8, 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: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057903 none CC1=C(C)OC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 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
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, 28, 28, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 41, 41, 41, 41, 41, 41, 41, 28, 8, 5, 1, 1, 1, 1] 41
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 78
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057903 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057903
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057903/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057903
Building REAL300000057904
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057904'
/scratch/stefan/7769638/working/building/REAL300000057904 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057904

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057904/0 /scratch/stefan/7769638/working/building/REAL300000057904 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 941)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/941
`/scratch/stefan/7769638/working/3D/941' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(CC3CC3)S2)C=C1)

`REAL300000057904.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057904.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057904/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057904 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(CC3CC3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 11, 18, 18, 18, 50, 50, 106, 106, 106, 106, 172, 201, 201, 106, 1, 1, 1, 1, 11, 18, 50, 106, 106, 172, 172, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 665
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057904 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(CC3CC3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 97, 106, 94, 106, 106, 82, 32, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 8, 25, 25, 1, 106, 106, 106, 106, 82, 32, 9, 1, 1, 8, 8, 25, 25, 25, 25, 25, 106, 106] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 411
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057904 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(CC3CC3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 196, 133, 133, 133, 80, 80, 25, 25, 25, 25, 5, 1, 1, 1, 1, 25, 201, 201, 201, 201, 196, 133, 80, 25, 25, 5, 5, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39])
total number of confs: 558
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057904 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057904
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057904/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057904
Building REAL300000057905
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057905'
/scratch/stefan/7769638/working/building/REAL300000057905 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057905

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057905/0 /scratch/stefan/7769638/working/building/REAL300000057905 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 942)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/942
`/scratch/stefan/7769638/working/3D/942' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1)

`REAL300000057905.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057905.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057905/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057905 none COC(=O)C1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 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]
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: [4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 10, 10, 27, 31, 31, 27, 27, 31, 31, 31, 31, 1, 4, 4, 4, 1, 1, 1, 9, 27, 31, 31, 31, 31, 1, 1] 74
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 34, 21, 25, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057905 none COC(=O)C1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 31, 74, 31, 31, 31, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 74, 74, 74, 31, 31, 31, 15, 7, 1, 1, 1, 1, 31, 31] 74
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, 34, 35])
total number of confs: 199
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057905 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057905
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057905/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057905
Building REAL300000057906
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057906'
/scratch/stefan/7769638/working/building/REAL300000057906 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057906

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057906/0 /scratch/stefan/7769638/working/building/REAL300000057906 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 943)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/943
`/scratch/stefan/7769638/working/3D/943' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3CC3)C=C2)C=C1)

`REAL300000057906.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057906.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057906/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057906 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3CC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 43, 43, 63, 63, 43, 43, 130, 148, 148, 63, 63, 1, 1, 1, 1, 8, 14, 43, 63, 63, 148, 148, 148, 148, 148, 63, 63, 1, 1] 148
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 351
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057906 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3CC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [63, 57, 63, 57, 63, 63, 50, 21, 20, 21, 5, 5, 1, 1, 1, 1, 1, 1, 13, 41, 41, 1, 1, 63, 63, 63, 63, 50, 20, 5, 1, 1, 41, 41, 41, 41, 41, 1, 1, 63, 63] 147
rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 287
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057906 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC3CC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [147, 147, 147, 147, 147, 147, 146, 101, 101, 101, 64, 64, 23, 18, 41, 41, 10, 1, 1, 1, 1, 41, 41, 147, 147, 147, 147, 146, 101, 63, 41, 41, 1, 1, 1, 1, 1, 41, 41, 147, 147] 147
rigid atoms, others: [32, 33, 34, 35, 36, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40])
total number of confs: 474
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057906 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057906
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057906/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057906
Building REAL300000057907
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057907'
/scratch/stefan/7769638/working/building/REAL300000057907 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057907

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057907/0 /scratch/stefan/7769638/working/building/REAL300000057907 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 944)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/944
`/scratch/stefan/7769638/working/3D/944' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC(F)(F)F)C=C2F)C=C1)

`REAL300000057907.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057907.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057907/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057907 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC(F)(F)F)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 15, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
200  conformations in input
total number of sets (complete confs): 200
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 18, 18, 18, 48, 48, 86, 86, 51, 86, 200, 200, 200, 200, 86, 86, 86, 1, 1, 1, 1, 10, 18, 48, 86, 86, 86, 1, 1] 200
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 25, 26, 27, 28, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34])
total number of confs: 446
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057907 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(OC(F)(F)F)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.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, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 15, 1, 1, 7, 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, 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: [88, 73, 88, 72, 88, 88, 72, 33, 32, 33, 12, 12, 1, 1, 1, 1, 1, 1, 12, 30, 30, 30, 1, 1, 1, 88, 88, 88, 88, 72, 32, 12, 1, 1, 1, 88, 88] 201
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 35, 36])
total number of confs: 387
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057907 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057907
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057907/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057907
Building REAL300000057908
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057908'
/scratch/stefan/7769638/working/building/REAL300000057908 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057908

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057908/0 /scratch/stefan/7769638/working/building/REAL300000057908 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 945)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/945
`/scratch/stefan/7769638/working/3D/945' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=CN1C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1)

`REAL300000057908.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057908/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057908 none CC1=NC=CN1C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 23, 35, 83, 83, 83, 143, 143, 143, 143, 143, 143, 143, 143, 143, 7, 7, 7, 2, 2, 2, 1, 1, 7, 7, 22, 83, 143, 143, 143, 143, 143, 7, 7, 7, 7] 143
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 403
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057908 none CC1=NC=CN1C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 11, 25, 42, 42, 42, 42, 42, 2, 2, 2, 1] 143
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 45, 25, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 124
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057908 none CC1=NC=CN1C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 143, 143, 42, 34, 42, 42, 28, 28, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 42, 42, 42, 143, 143, 143, 143, 143, 42, 42, 28, 14, 7, 1, 1, 1, 1, 42, 42, 42, 42] 143
rigid atoms, others: [38, 39, 40, 41, 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, 36, 37, 42, 43, 44, 45])
total number of confs: 256
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057908 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057908
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057908/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057908
Building REAL300000057909
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057909'
/scratch/stefan/7769638/working/building/REAL300000057909 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057909

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057909/0 /scratch/stefan/7769638/working/building/REAL300000057909 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 946)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/946
`/scratch/stefan/7769638/working/3D/946' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)N(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C2)C=N1)

`REAL300000057909.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057909/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057909 none CC1=C(C)N(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 5, 5, 17, 17, 17, 17, 17, 3, 3, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057909 none CC1=C(C)N(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 9, 9, 9, 9, 9, 1, 1, 3] 17
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 43, 44, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 45])
total number of confs: 26
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057909 none CC1=C(C)N(C2=CC=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 5, 5, 3, 1, 1, 1, 1, 9, 9, 17] 17
rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45])
total number of confs: 43
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057909 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057909
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057909/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057909
Building REAL300000057910
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057910'
/scratch/stefan/7769638/working/building/REAL300000057910 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057910

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057910/0 /scratch/stefan/7769638/working/building/REAL300000057910 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 947)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/947
`/scratch/stefan/7769638/working/3D/947' -> `0.mol2'
Preparing input files

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

`REAL300000057910.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057910.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057910/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057910 none CNC(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 23, 23, 23, 49, 53, 53, 49, 51, 53, 53, 53, 53, 1, 7, 7, 7, 7, 1, 1, 1, 9, 23, 49, 53, 53, 53, 53, 1] 72
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 39, 24, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057910 none CNC(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 53, 72, 53, 53, 53, 53, 22, 22, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 72, 72, 72, 72, 53, 53, 53, 22, 10, 7, 1, 1, 1, 1, 53] 72
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, 39])
total number of confs: 159
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057910 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057910
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057910/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057910
Building REAL300000057911
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057911'
/scratch/stefan/7769638/working/building/REAL300000057911 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057911

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057911/0 /scratch/stefan/7769638/working/building/REAL300000057911 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 948)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/948
`/scratch/stefan/7769638/working/3D/948' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)COCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057911.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057911.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057911/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057911 none CC1(C)COCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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
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, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39])
total number of confs: 57
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057911 none CC1(C)COCCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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
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, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 7, 1, 1, 1, 1] 19
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 46
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057911 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057911
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057911/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057911
Building REAL300000057912
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057912'
/scratch/stefan/7769638/working/building/REAL300000057912 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057912

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057912/0 /scratch/stefan/7769638/working/building/REAL300000057912 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 949)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/949
`/scratch/stefan/7769638/working/3D/949' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOCC23CCCC3)C=C1)

`REAL300000057912.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057912/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057912 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOCC23CCCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 15, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 8, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1] 22
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 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, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 60
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057912 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOCC23CCCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 22
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 43, 22, 23, 24, 25, 26, 27])
total number of confs: 57
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057912 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057912
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057912/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057912
Building REAL300000057913
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057913'
/scratch/stefan/7769638/working/building/REAL300000057913 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057913

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057913/0 /scratch/stefan/7769638/working/building/REAL300000057913 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 950)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/950
`/scratch/stefan/7769638/working/3D/950' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C(=O)[O-])

`REAL300000057913.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057913.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057913/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057913 none COC1=CC=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 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
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 12, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 2, 2, 3, 3, 3, 1, 1, 2, 2, 2, 4, 7, 12, 14, 14, 14, 14] 14
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])
total number of confs: 52
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057913 none COC1=CC=C(C)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 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
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 5, 5, 1, 1, 1, 1] 14
rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 32
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057913 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057913
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057913/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057913
Building REAL300000057914
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057914'
/scratch/stefan/7769638/working/building/REAL300000057914 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057914

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057914/0 /scratch/stefan/7769638/working/building/REAL300000057914 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 951)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/951
`/scratch/stefan/7769638/working/3D/951' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1C(=O)[O-])

`REAL300000057914.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057914.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057914/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057914 none CN1C2=CC=C(F)C=C2C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 4, 4, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 5, 6, 6, 6, 6, 6] 6
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])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057914 none CN1C2=CC=C(F)C=C2C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1] 6
rigid atoms, others: [38, 39, 40, 41, 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, 36, 37])
total number of confs: 16
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057914 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057914
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057914/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057914
Building REAL300000057915
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057915'
/scratch/stefan/7769638/working/building/REAL300000057915 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057915

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057915/0 /scratch/stefan/7769638/working/building/REAL300000057915 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 952)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/952
`/scratch/stefan/7769638/working/3D/952' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3CC3)C(C3CC3)=C2)C=C1)

`REAL300000057915.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057915/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057915 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3CC3)C(C3CC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 17, 17, 17, 47, 47, 115, 115, 75, 115, 172, 172, 115, 115, 173, 173, 115, 1, 1, 1, 1, 8, 17, 47, 115, 115, 172, 172, 172, 172, 172, 173, 173, 173, 173, 173, 115, 1, 1] 183
rigid atoms, others: [1, 3, 4, 5, 6, 7, 45, 46, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 775
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057915 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3CC3)C(C3CC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [176, 175, 176, 175, 176, 176, 171, 90, 90, 90, 38, 38, 8, 8, 7, 8, 8, 8, 16, 16, 1, 1, 1, 1, 8, 176, 176, 176, 176, 171, 90, 38, 7, 8, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 8, 176, 176] 186
rigid atoms, others: [39, 40, 41, 42, 43, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 509
number of broken/clashed sets: 5
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057915 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3CC3)C(C3CC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [118, 109, 118, 108, 118, 118, 100, 41, 41, 41, 12, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 8, 8, 1, 118, 118, 118, 118, 100, 41, 12, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 1, 118, 118] 186
rigid atoms, others: [32, 33, 44, 12, 13, 14, 15, 16, 17, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46])
total number of confs: 396
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057915 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=C(C3CC3)C(C3CC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [175, 172, 175, 172, 175, 175, 167, 83, 83, 83, 33, 33, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 16, 16, 6, 175, 175, 175, 175, 167, 83, 33, 6, 6, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 6, 175, 175] 186
rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 545
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057915 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057915
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057915/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057915
Building REAL300000057916
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057916'
/scratch/stefan/7769638/working/building/REAL300000057916 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057916

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057916/0 /scratch/stefan/7769638/working/building/REAL300000057916 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 953)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/953
`/scratch/stefan/7769638/working/3D/953' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000057916.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057916.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057916/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057916 none C[NH+](C)CCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 9, 6, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [5, 3, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 5, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 6, 8, 17, 17, 17, 17, 17, 1, 1] 21
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 46, 47, 25, 4, 26, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 67
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057916 none C[NH+](C)CCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 9, 6, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 17, 7, 7, 17, 17, 7, 7, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 17, 17, 17, 17, 7, 5, 3, 1, 1, 1, 1, 17, 17] 21
rigid atoms, others: [42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47])
total number of confs: 117
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057916 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057916
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057916/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057916
Building REAL300000057917
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057917'
/scratch/stefan/7769638/working/building/REAL300000057917 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057917

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057917/0 /scratch/stefan/7769638/working/building/REAL300000057917 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 954)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/954
`/scratch/stefan/7769638/working/3D/954' -> `0.mol2'
Preparing input files

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

`REAL300000057917.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057917/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057917 none CCNC(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 63, 84, 84, 63, 73, 84, 84, 84, 84, 1, 19, 19, 19, 19, 19, 7, 1, 1, 1, 9, 29, 63, 84, 84, 84, 84, 1] 175
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 25, 42] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 387
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057917 none CCNC(=O)C1=CC=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [175, 135, 135, 84, 135, 84, 84, 84, 84, 34, 34, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 175, 175, 175, 175, 175, 135, 84, 84, 84, 34, 14, 7, 1, 1, 1, 1, 84] 175
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 564
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057917 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057917
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057917/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057917
Building REAL300000057918
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057918'
/scratch/stefan/7769638/working/building/REAL300000057918 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057918

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057918/0 /scratch/stefan/7769638/working/building/REAL300000057918 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 955)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/955
`/scratch/stefan/7769638/working/3D/955' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)OC2=CC=C(F)C=C12)

`REAL300000057918.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057918.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057918/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057918 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)OC2=CC=C(F)C=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 8, 8, 22, 22, 22, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 22, 64, 64, 64, 64, 64, 1, 1, 1] 64
rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 18, 19, 20, 21, 22, 23, 24, 25] set([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: 179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057918 none CC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)OC2=CC=C(F)C=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 38, 38, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 38, 14, 7, 1, 1, 1, 1, 64, 64, 64] 64
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 117
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057918 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057918
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057918/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057918
Building REAL300000057919
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057919'
/scratch/stefan/7769638/working/building/REAL300000057919 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057919

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057919/0 /scratch/stefan/7769638/working/building/REAL300000057919 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 956)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/956
`/scratch/stefan/7769638/working/3D/956' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN3C=CN=C23)C=C1)

`REAL300000057919.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057919.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057919/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057919 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN3C=CN=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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, 9, 12, 12, 12, 24, 24, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 9, 12, 24, 28, 28, 28, 28, 28, 1, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 52
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057919 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CN3C=CN=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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, 17, 17, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 17, 9, 1, 1, 1, 1, 1, 34, 34] 34
rigid atoms, others: [32, 33, 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, 34, 35, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057919 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057919
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057919/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057919
Building REAL300000057920
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057920'
/scratch/stefan/7769638/working/building/REAL300000057920 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057920

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057920/0 /scratch/stefan/7769638/working/building/REAL300000057920 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 957)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/957
`/scratch/stefan/7769638/working/3D/957' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(C(F)(F)F)=CN2)C=C1)

`REAL300000057920.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057920/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057920 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(C(F)(F)F)=CN2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 5, 15, 15, 15, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 6, 8, 22, 22, 22, 1, 1] 22
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057920 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC(C(F)(F)F)=CN2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 5, 15, 15, 15, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 22, 22, 22, 22, 22, 8, 4, 1, 1, 22, 22] 22
rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 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: 67
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057920 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057920/1 /scratch/stefan/7769638/working/building/REAL300000057920 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 958)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/958
`/scratch/stefan/7769638/working/3D/958' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(C(F)(F)F)N2)C=C1)

`REAL300000057920.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057920/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057920 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(C(F)(F)F)N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 6, 6, 7, 7, 6, 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, 4, 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, 8, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 8, 10, 20, 20, 20, 1, 1] 20
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057920 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(C(F)(F)F)N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 6, 6, 7, 7, 6, 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, 4, 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, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 20, 20, 20, 20, 20, 10, 4, 1, 1, 20, 20] 20
rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 59
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057920 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057920
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057920/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057920/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057920
Building REAL300000057921
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057921'
/scratch/stefan/7769638/working/building/REAL300000057921 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057921

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057921/0 /scratch/stefan/7769638/working/building/REAL300000057921 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 959)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/959
`/scratch/stefan/7769638/working/3D/959' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NNC(C3CCC3)=C2)C=C1)

`REAL300000057921.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057921.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057921/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057921 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NNC(C3CCC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 15, 15, 15, 42, 42, 65, 65, 65, 65, 111, 111, 111, 65, 1, 1, 1, 1, 8, 15, 42, 65, 111, 111, 111, 111, 111, 111, 111, 65, 1, 1] 111
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 271
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057921 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NNC(C3CCC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [67, 62, 67, 59, 67, 67, 59, 27, 26, 27, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 1, 67, 67, 67, 67, 59, 26, 7, 1, 12, 12, 12, 12, 12, 12, 12, 1, 67, 67] 116
rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 38, 39])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057921 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NNC(C3CCC3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [116, 116, 116, 115, 116, 116, 115, 72, 72, 72, 37, 37, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 116, 116, 116, 116, 115, 72, 37, 12, 1, 1, 1, 1, 1, 1, 1, 12, 116, 116] 116
rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39])
total number of confs: 322
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057921 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057921
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057921/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057921
Building REAL300000057922
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057922'
/scratch/stefan/7769638/working/building/REAL300000057922 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057922

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057922/0 /scratch/stefan/7769638/working/building/REAL300000057922 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 960)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/960
`/scratch/stefan/7769638/working/3D/960' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(F)C=C2F)C=C1)

`REAL300000057922.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057922.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057922/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057922 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(F)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 8, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 35, 35, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 8, 13, 35, 49, 49, 1, 1] 49
rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057922 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC=C(F)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 8, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 19, 18, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 18, 6, 1, 1, 57, 57] 57
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057922 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057922
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057922/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057922
Building REAL300000057923
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057923'
/scratch/stefan/7769638/working/building/REAL300000057923 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057923

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057923/0 /scratch/stefan/7769638/working/building/REAL300000057923 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 961)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/961
`/scratch/stefan/7769638/working/3D/961' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CC=C(Cl)C=C1F)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057923.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057923.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057923/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057923 none CC(CC1=CC=C(Cl)C=C1F)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 16, 1, 1, 15, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 49, 49, 49, 49, 49, 49, 49, 49, 49, 11, 11, 11, 5, 5, 1, 1, 1, 25, 49, 49, 49, 49, 49] 49
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 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])
total number of confs: 164
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057923 none CC(CC1=CC=C(Cl)C=C1F)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 16, 1, 1, 15, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 15, 15, 15, 49, 49, 49, 49, 49, 5, 3, 1, 1, 1, 1] 49
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])
total number of confs: 177
number of broken/clashed sets: 45
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057923 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057923
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057923/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057923
Building REAL300000057924
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057924'
/scratch/stefan/7769638/working/building/REAL300000057924 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057924

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057924/0 /scratch/stefan/7769638/working/building/REAL300000057924 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 962)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/962
`/scratch/stefan/7769638/working/3D/962' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C2=CC=CC=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057924.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057924.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057924/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057924 none CN1N=C(C2=CC=CC=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 6, 6, 1, 6, 6, 1, 1, 1, 8, 8, 29, 30, 30, 69, 76, 76, 73, 73, 76, 76, 76, 76, 2, 2, 2, 6, 6, 1, 6, 6, 1, 8, 29, 69, 76, 76, 76, 76] 111
rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 35] set([5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057924 none CN1N=C(C2=CC=CC=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 33, 33, 72, 72, 72, 107, 111, 111, 111, 111, 111, 111, 111, 111, 7, 7, 7, 1, 1, 1, 1, 1, 6, 32, 72, 107, 111, 111, 111, 111] 111
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 326
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057924 none CN1N=C(C2=CC=CC=C2)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 76, 76, 111, 111, 76, 111, 111, 76, 36, 36, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 111, 111, 111, 111, 111, 76, 36, 12, 7, 1, 1, 1, 1] 111
rigid atoms, others: [39, 40, 41, 42, 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])
total number of confs: 367
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057924 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057924
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057924/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057924
Building REAL300000057925
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057925'
/scratch/stefan/7769638/working/building/REAL300000057925 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057925

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057925/0 /scratch/stefan/7769638/working/building/REAL300000057925 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 963)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/963
`/scratch/stefan/7769638/working/3D/963' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057925.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057925.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057925/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057925 none CCCN1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [17, 9, 1, 1, 1, 1, 1, 1, 8, 8, 24, 25, 25, 53, 71, 71, 53, 53, 71, 71, 71, 71, 1, 17, 17, 17, 17, 17, 9, 9, 1, 1, 8, 24, 53, 71, 71, 71, 71] 140
rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 338
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057925 none CCCN1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [140, 140, 71, 71, 71, 71, 48, 48, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 71, 140, 140, 140, 140, 140, 140, 140, 71, 71, 48, 18, 7, 1, 1, 1, 1] 140
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 439
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057925 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057925
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057925/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057925
Building REAL300000057926
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057926'
/scratch/stefan/7769638/working/building/REAL300000057926 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057926

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057926/0 /scratch/stefan/7769638/working/building/REAL300000057926 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 964)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/964
`/scratch/stefan/7769638/working/3D/964' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)N1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1)

`REAL300000057926.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057926.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057926/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057926 none CC(C)N1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [11, 1, 11, 1, 1, 1, 1, 1, 7, 7, 21, 22, 22, 55, 60, 60, 55, 57, 60, 60, 60, 60, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 7, 21, 55, 60, 60, 60, 60] 66
rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057926 none CC(C)N1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 60, 66, 60, 60, 60, 46, 46, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 60, 66, 66, 66, 66, 66, 66, 66, 60, 60, 46, 16, 7, 1, 1, 1, 1] 66
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 143
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057926 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057926
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057926/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057926
Building REAL300000057927
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057927'
/scratch/stefan/7769638/working/building/REAL300000057927 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057927

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057927/0 /scratch/stefan/7769638/working/building/REAL300000057927 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 965)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/965
`/scratch/stefan/7769638/working/3D/965' -> `0.mol2'
Preparing input files

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

`REAL300000057927.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057927.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057927/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057927 none CC(C)(C)C1=CN=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 39, 39, 39, 93, 107, 107, 97, 102, 107, 107, 107, 107, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 8, 38, 93, 107, 107, 107, 107, 1] 107
rigid atoms, others: [1, 34, 35, 4, 5, 6, 7, 8, 9, 43, 24] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 342
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057927 none CC(C)(C)C1=CN=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 48, 48, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 48, 18, 7, 1, 1, 1, 1, 107] 107
rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057927 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057927
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057927/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057927
Building REAL300000057928
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057928'
/scratch/stefan/7769638/working/building/REAL300000057928 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057928

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057928/0 /scratch/stefan/7769638/working/building/REAL300000057928 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 966)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/966
`/scratch/stefan/7769638/working/3D/966' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1C=CCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057928.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057928/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057928 none CC(CC1C=CCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [40, 10, 1, 1, 1, 1, 1, 1, 40, 40, 114, 114, 114, 179, 182, 182, 179, 179, 182, 182, 182, 182, 40, 40, 40, 10, 10, 1, 1, 1, 1, 1, 1, 1, 114, 179, 182, 182, 182, 182] 182
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30, 31] set([0, 1, 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])
total number of confs: 552
number of broken/clashed sets: 115
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057928 none CC(CC1C=CCC1)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 158, 182, 182, 182, 182, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 60, 60, 60, 158, 158, 182, 182, 182, 182, 182, 182, 182, 18, 7, 1, 1, 1, 1] 182
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 609
number of broken/clashed sets: 115
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057928 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057928
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057928/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057928
Building REAL300000057929
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057929'
/scratch/stefan/7769638/working/building/REAL300000057929 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000057929

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057929/0 /scratch/stefan/7769638/working/building/REAL300000057929 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 967)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/967
`/scratch/stefan/7769638/working/3D/967' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C([O-])=C1F)

`REAL300000057929.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057929/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057929 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C([O-])=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 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, 2, 2, 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: [31, 31, 17, 17, 6, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 31, 47, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 17, 6, 1, 1, 1, 1, 47, 47] 47
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 101
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057929 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C([O-])=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 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, 2, 2, 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: [9, 1, 9, 9, 27, 27, 27, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 47, 47, 47, 47, 47, 1, 1] 47
rigid atoms, others: [1, 34, 35, 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])
total number of confs: 127
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057929 /scratch/stefan/7769638/working /scratch/stefan/7769638
mkdir: created directory `1'
/scratch/stefan/7769638/working/building/REAL300000057929/1 /scratch/stefan/7769638/working/building/REAL300000057929 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 1 (index: 968)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/968
`/scratch/stefan/7769638/working/3D/968' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C(O)=C1F)

`REAL300000057929.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000057929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057929/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057929 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C(O)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 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]
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: [27, 27, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 45, 45, 45, 45, 45, 45, 45, 45, 27, 27, 27, 15, 7, 1, 1, 1, 1, 45, 45, 90] 90
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 185
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057929 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C(O)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 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]
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, 9, 27, 27, 27, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 45, 45, 45, 45, 45, 1, 1, 2] 90
rigid atoms, others: [1, 34, 35, 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, 36])
total number of confs: 129
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057929 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057929
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057929/0.*
1: /scratch/stefan/7769638/working/building/REAL300000057929/1.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057929
Building REAL300000057930
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057930'
/scratch/stefan/7769638/working/building/REAL300000057930 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057930

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057930/0 /scratch/stefan/7769638/working/building/REAL300000057930 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 969)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/969
`/scratch/stefan/7769638/working/3D/969' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC1=O)

`REAL300000057930.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057930.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057930/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057930 none CN1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 13, 13, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 1, 13, 29, 50, 50, 50, 50, 50, 1] 50
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: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057930 none CN1C=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 29, 29, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 29, 13, 7, 1, 1, 1, 1, 50] 50
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 100
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057930 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057930
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057930/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057930
Building REAL300000057931
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057931'
/scratch/stefan/7769638/working/building/REAL300000057931 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057931

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057931/0 /scratch/stefan/7769638/working/building/REAL300000057931 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 970)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/970
`/scratch/stefan/7769638/working/3D/970' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(Cl)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1N)

`REAL300000057931.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057931.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057931/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057931 none CC1=CC=C(Cl)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 16, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 10, 10, 28, 28, 28, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 2, 2, 2, 1, 1, 10, 28, 37, 37, 37, 37, 37, 2, 2] 37
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 27, 28] set([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: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057931 none CC1=CC=C(Cl)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 16, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 32, 37, 37, 37, 23, 23, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 37, 37, 23, 15, 7, 1, 1, 1, 1, 37, 37] 37
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
total number of confs: 100
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057931 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057931
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057931/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057931
Building REAL300000057932
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057932'
/scratch/stefan/7769638/working/building/REAL300000057932 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057932

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057932/0 /scratch/stefan/7769638/working/building/REAL300000057932 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 971)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/971
`/scratch/stefan/7769638/working/3D/971' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NNC2=CS(=O)(=O)C3=CC=CC=C23)C=C1)

`REAL300000057932.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057932.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057932/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057932 none O=C([O-])C1=CC=C(NC(=O)NNC2=CS(=O)(=O)C3=CC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', '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, 8, 1, 11, 8, 8, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 4, 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
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, 20, 20, 20, 65, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 1, 1, 1, 1, 9, 20, 65, 118, 118, 118, 118, 118, 1, 1] 118
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 23, 24, 25, 26, 36] set([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: 245
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057932 none O=C([O-])C1=CC=C(NC(=O)NNC2=CS(=O)(=O)C3=CC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', '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, 8, 1, 11, 8, 8, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 4, 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
185  conformations in input
total number of sets (complete confs): 185
using faster count positions algorithm for large data
unique positions, atoms: [185, 185, 185, 185, 185, 185, 182, 69, 68, 69, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 182, 68, 11, 1, 1, 1, 1, 1, 185, 185] 185
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 503
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057932 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057932
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057932/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057932
Building REAL300000057933
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057933'
/scratch/stefan/7769638/working/building/REAL300000057933 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057933

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057933/0 /scratch/stefan/7769638/working/building/REAL300000057933 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 972)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/972
`/scratch/stefan/7769638/working/3D/972' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(CF)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000057933.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057933.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057933/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057933 none N#CC1=CC=C(C(CF)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 5, 15, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 28, 7, 7, 30, 30, 30, 71, 75, 75, 71, 71, 75, 75, 75, 75, 1, 1, 1, 1, 28, 28, 30, 71, 75, 75, 75, 75, 1, 1] 75
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 23, 24, 25, 26, 36] set([7, 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: 307
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057933 none N#CC1=CC=C(C(CF)=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 5, 15, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 11, 11, 6, 6, 6, 11, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 5, 3, 1, 1, 1, 1, 11, 11] 11
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 70
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057933 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057933
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057933/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057933
Building REAL300000057934
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057934'
/scratch/stefan/7769638/working/building/REAL300000057934 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057934

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057934/0 /scratch/stefan/7769638/working/building/REAL300000057934 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 973)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/973
`/scratch/stefan/7769638/working/3D/973' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C2CC2)N=C1)

`REAL300000057934.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057934.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057934/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057934 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C2CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 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: [49, 49, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 49, 115, 115, 115, 151, 151, 115, 115, 49, 49, 49, 18, 7, 1, 1, 1, 1, 115, 151, 151, 151, 151, 151, 115] 151
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 332
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057934 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C2CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 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: [12, 1, 12, 12, 52, 52, 52, 103, 115, 115, 103, 111, 115, 115, 115, 115, 1, 1, 1, 1, 12, 12, 1, 1, 13, 13, 13, 51, 103, 115, 115, 115, 115, 1, 12, 12, 12, 12, 12, 1] 151
rigid atoms, others: [1, 33, 39, 16, 17, 18, 19, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 392
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057934 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C2CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 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: [75, 12, 75, 75, 123, 123, 123, 150, 151, 151, 150, 151, 151, 151, 151, 151, 12, 12, 1, 1, 1, 1, 12, 12, 75, 75, 75, 123, 150, 151, 151, 151, 151, 12, 1, 1, 1, 1, 1, 12] 151
rigid atoms, others: [34, 35, 36, 37, 38, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39])
total number of confs: 406
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057934 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057934
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057934/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057934
Building REAL300000057935
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057935'
/scratch/stefan/7769638/working/building/REAL300000057935 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057935

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057935/0 /scratch/stefan/7769638/working/building/REAL300000057935 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 974)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/974
`/scratch/stefan/7769638/working/3D/974' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2N2C=CC=N2)C=C1)

`REAL300000057935.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057935.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057935/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057935 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2N2C=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 1, 8, 14, 14, 14, 31, 31, 90, 90, 47, 90, 90, 90, 113, 113, 113, 113, 1, 1, 1, 1, 8, 14, 31, 90, 90, 90, 90, 113, 113, 113, 1, 1] 113
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057935 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2N2C=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 10, 10, 10, 10, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 10, 6, 5, 1, 1, 1, 1, 4, 4, 4, 10, 10] 10
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057935 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC=C2N2C=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 10, 10, 10, 10, 6, 6, 6, 5, 5, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 6, 5, 4, 4, 4, 4, 1, 1, 1, 10, 10] 10
rigid atoms, others: [35, 36, 37, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39])
total number of confs: 36
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057935 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057935
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057935/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057935
Building REAL300000057936
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057936'
/scratch/stefan/7769638/working/building/REAL300000057936 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057936

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057936/0 /scratch/stefan/7769638/working/building/REAL300000057936 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 975)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/975
`/scratch/stefan/7769638/working/3D/975' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN(CC(F)(F)F)C=C2)C=C1)

`REAL300000057936.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057936.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057936/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057936 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN(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', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', '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, 11, 8, 8, 1, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 6, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 38, 38, 55, 55, 55, 95, 95, 95, 95, 55, 55, 1, 1, 1, 1, 8, 12, 38, 95, 95, 55, 55, 1, 1] 95
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: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057936 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NN(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', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', '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, 11, 8, 8, 1, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 6, 7, 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, 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: [53, 49, 53, 47, 53, 53, 47, 21, 21, 21, 9, 9, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 53, 53, 53, 53, 47, 21, 9, 9, 9, 1, 1, 53, 53] 97
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057936 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057936
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057936/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057936
Building REAL300000057937
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057937'
/scratch/stefan/7769638/working/building/REAL300000057937 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057937

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057937/0 /scratch/stefan/7769638/working/building/REAL300000057937 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 976)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/976
`/scratch/stefan/7769638/working/3D/976' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC([N+](=O)[O-])=CC=C23)C=C1)

`REAL300000057937.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057937/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057937 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC([N+](=O)[O-])=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 3, 5, 5, 13, 13, 13, 13, 13, 1, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 25, 26, 27, 28, 37] set([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])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057937 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNC3=CC([N+](=O)[O-])=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 74, 74, 74, 73, 30, 29, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 73, 29, 10, 1, 1, 1, 1, 1, 74, 74] 74
rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 37, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 191
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057937 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057937
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057937/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057937
Building REAL300000057938
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057938'
/scratch/stefan/7769638/working/building/REAL300000057938 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057938

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057938/0 /scratch/stefan/7769638/working/building/REAL300000057938 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 977)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/977
`/scratch/stefan/7769638/working/3D/977' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2C2=C(C=CC=C2)N3)C=C1)

`REAL300000057938.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057938/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057938 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2C2=C(C=CC=C2)N3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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, 3, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 3, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1] 15
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 33
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057938 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2C2=C(C=CC=C2)N3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 31, 31, 31, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 31, 10, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72] 72
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 42, 32, 41, 26, 27, 28, 29, 30, 31])
total number of confs: 195
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057938 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057938
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057938/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057938
Building REAL300000057939
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057939'
/scratch/stefan/7769638/working/building/REAL300000057939 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057939

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057939/0 /scratch/stefan/7769638/working/building/REAL300000057939 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 978)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/978
`/scratch/stefan/7769638/working/3D/978' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NC2=C1CCCC2)

`REAL300000057939.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057939.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057939/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057939 none CN1C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 10, 22, 22, 22, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 22, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1] 43
rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24, 38] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057939 none CN1C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=NC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 28, 28, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 28, 12, 7, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43] 43
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 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: 82
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057939 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057939
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057939/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057939
Building REAL300000057940
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057940'
/scratch/stefan/7769638/working/building/REAL300000057940 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057940

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057940/0 /scratch/stefan/7769638/working/building/REAL300000057940 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 979)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/979
`/scratch/stefan/7769638/working/3D/979' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NC(Cl)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057940.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057940.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057940/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057940 none COC1=NC(Cl)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 8, 1, 16, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 6, 6, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 6, 10, 22, 22, 22, 22, 22] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28] set([32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057940 none COC1=NC(Cl)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 8, 1, 16, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 12, 7, 1, 1, 1, 1] 22
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])
total number of confs: 44
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057940 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057940
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057940/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057940
Building REAL300000057941
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057941'
/scratch/stefan/7769638/working/building/REAL300000057941 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057941

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057941/0 /scratch/stefan/7769638/working/building/REAL300000057941 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 980)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/980
`/scratch/stefan/7769638/working/3D/980' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C(F)(F)F)=N1)

`REAL300000057941.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057941/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057941 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C(F)(F)F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 8, 8, 24, 24, 24, 53, 54, 54, 53, 53, 54, 54, 54, 54, 1, 1, 2, 2, 2, 1, 2, 2, 2, 1, 8, 24, 53, 54, 54, 54, 54] 54
rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 166
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057941 none CN1C=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C(C(F)(F)F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 47, 47, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 47, 18, 7, 1, 1, 1, 1] 54
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057941 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057941
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057941/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057941
Building REAL300000057942
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057942'
/scratch/stefan/7769638/working/building/REAL300000057942 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057942

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057942/0 /scratch/stefan/7769638/working/building/REAL300000057942 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 981)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/981
`/scratch/stefan/7769638/working/3D/981' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCOC2=C1C)

`REAL300000057942.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057942.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057942/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057942 none CC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCOC2=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 1, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 8, 16, 16, 16, 16, 16, 1, 1, 1, 1, 2, 2, 2] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 20, 21, 22, 23, 24, 25, 38, 29, 30, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 53
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057942 none CC1=CC=C2C(=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)CCOC2=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 1, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 7, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16] 16
rigid atoms, others: [33, 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, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 38
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057942 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057942
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057942/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057942
Building REAL300000057943
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057943'
/scratch/stefan/7769638/working/building/REAL300000057943 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057943

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057943/0 /scratch/stefan/7769638/working/building/REAL300000057943 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 982)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/982
`/scratch/stefan/7769638/working/3D/982' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Br)=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057943.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057943.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057943/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057943 none CC1=CC(Br)=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 17, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 1, 1, 1, 13, 13, 23, 23, 23, 36, 36, 36, 36, 36, 36, 36, 36, 36, 2, 2, 2, 1, 1, 13, 23, 36, 36, 36, 36, 36] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057943 none CC1=CC(Br)=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 17, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 22, 22, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 36, 36, 36, 36, 22, 10, 7, 1, 1, 1, 1] 36
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057943 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057943
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057943/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057943
Building REAL300000057944
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057944'
/scratch/stefan/7769638/working/building/REAL300000057944 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057944

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057944/0 /scratch/stefan/7769638/working/building/REAL300000057944 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 983)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/983
`/scratch/stefan/7769638/working/3D/983' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=CC=C3C=N2)C=C1)

`REAL300000057944.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057944/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057944 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=CC=C3C=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 5
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: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057944 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=CC=C3C=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 8, 6, 1, 1, 1, 1, 1, 1, 25, 25] 25
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 37, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 65
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057944 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057944
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057944/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057944
Building REAL300000057945
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057945'
/scratch/stefan/7769638/working/building/REAL300000057945 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057945

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057945/0 /scratch/stefan/7769638/working/building/REAL300000057945 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 984)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/984
`/scratch/stefan/7769638/working/3D/984' -> `0.mol2'
Preparing input files

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

`REAL300000057945.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057945.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057945/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057945 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)[C@@H]1C[C@H]1C1=CC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 8, 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, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 80, 80, 80, 80, 80, 119, 119, 119, 119, 119, 30, 30, 30, 13, 7, 1, 1, 1, 1, 80, 80, 119, 119, 119, 119] 119
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 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: 271
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057945 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)[C@@H]1C[C@H]1C1=CC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 8, 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, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 33, 33, 33, 69, 80, 80, 69, 69, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 10, 10, 10, 33, 69, 80, 80, 80, 80, 1, 1, 11, 11, 11, 11] 119
rigid atoms, others: [1, 36, 37, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41])
total number of confs: 305
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057945 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)[C@@H]1C[C@H]1C1=CC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 8, 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, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [60, 11, 60, 60, 85, 85, 85, 119, 119, 119, 119, 119, 119, 119, 119, 119, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 60, 60, 60, 85, 119, 119, 119, 119, 119, 11, 11, 1, 1, 1, 1] 119
rigid atoms, others: [38, 39, 40, 41, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 351
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057945 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057945
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057945/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057945
Building REAL300000057946
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057946'
/scratch/stefan/7769638/working/building/REAL300000057946 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057946

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057946/0 /scratch/stefan/7769638/working/building/REAL300000057946 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 985)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/985
`/scratch/stefan/7769638/working/3D/985' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C(F)F)=C2F)C=C1)

`REAL300000057946.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057946/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057946 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C(F)F)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 1, 7, 7, 6, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 16, 16, 16, 36, 36, 62, 62, 43, 62, 62, 85, 85, 62, 62, 1, 1, 1, 1, 9, 16, 36, 62, 62, 62, 85, 1, 1] 85
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 23, 24, 25, 26] set([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: 300
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057946 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC(C(F)F)=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 1, 7, 7, 6, 6, 7, 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, 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: [58, 58, 58, 58, 58, 58, 55, 27, 26, 27, 12, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 58, 58, 58, 58, 55, 26, 12, 1, 1, 1, 8, 58, 58] 77
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 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
/scratch/stefan/7769638/working/building/REAL300000057946 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057946
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057946/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057946
Building REAL300000057947
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057947'
/scratch/stefan/7769638/working/building/REAL300000057947 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057947

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057947/0 /scratch/stefan/7769638/working/building/REAL300000057947 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 986)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/986
`/scratch/stefan/7769638/working/3D/986' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2COCC3)C=C1)

`REAL300000057947.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057947.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057947/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057947 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2COCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 35, 35, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 10, 14, 35, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1] 58
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 23, 24, 25, 26] set([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])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057947 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CC3=C2COCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 33, 33, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59] 59
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 23, 24, 25, 26, 27, 28, 29, 39])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057947 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057947
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057947/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057947
Building REAL300000057948
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057948'
/scratch/stefan/7769638/working/building/REAL300000057948 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057948

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057948/0 /scratch/stefan/7769638/working/building/REAL300000057948 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 987)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/987
`/scratch/stefan/7769638/working/3D/987' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C(Cl)C=CC(O)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057948.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057948.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057948/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057948 none COC(=O)C1=C(Cl)C=CC(O)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 1, 1, 16, 1, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 4, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 21, 23, 23, 22, 23, 23, 23, 23, 23, 7, 7, 7, 1, 1, 2, 4, 10, 21, 23, 23, 23, 23] 64
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 86
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057948 none COC(=O)C1=C(Cl)C=CC(O)=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 1, 1, 16, 1, 1, 1, 12, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 4, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 23, 32, 23, 23, 23, 23, 23, 23, 23, 15, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 32, 23, 23, 46, 15, 6, 6, 1, 1, 1, 1] 64
rigid atoms, others: [36, 37, 38, 39, 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])
total number of confs: 126
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057948 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057948
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057948/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057948
Building REAL300000057949
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057949'
/scratch/stefan/7769638/working/building/REAL300000057949 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057949

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057949/0 /scratch/stefan/7769638/working/building/REAL300000057949 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 988)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/988
`/scratch/stefan/7769638/working/3D/988' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC=C(Cl)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057949.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057949.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057949/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057949 none CCOC1=CC=C(Cl)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 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, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 49, 59, 59, 54, 59, 59, 59, 59, 59, 24, 24, 24, 24, 24, 1, 1, 1, 6, 20, 49, 59, 59, 59, 59] 98
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 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])
total number of confs: 242
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057949 none CCOC1=CC=C(Cl)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 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, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 94, 59, 59, 59, 38, 59, 59, 59, 38, 38, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 59, 59, 59, 38, 18, 7, 1, 1, 1, 1] 98
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])
total number of confs: 284
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057949 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057949
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057949/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057949
Building REAL300000057950
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057950'
/scratch/stefan/7769638/working/building/REAL300000057950 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057950

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057950/0 /scratch/stefan/7769638/working/building/REAL300000057950 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 989)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/989
`/scratch/stefan/7769638/working/3D/989' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NN(C)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057950.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057950.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057950/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057950 none COC1=NN(C)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 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, 4, 4, 12, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 1, 4, 12, 28, 28, 28, 28, 28] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057950 none COC1=NN(C)C=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 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, 26, 26, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 26, 12, 7, 1, 1, 1, 1] 28
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: 54
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057950 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057950
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057950/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057950
Building REAL300000057951
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057951'
/scratch/stefan/7769638/working/building/REAL300000057951 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057951

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057951/0 /scratch/stefan/7769638/working/building/REAL300000057951 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 990)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/990
`/scratch/stefan/7769638/working/3D/990' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN(CC(F)(F)F)C2)C=C1)

`REAL300000057951.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057951.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057951/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057951 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN(CC(F)(F)F)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 11, 11, 11, 28, 28, 28, 28, 28, 28, 48, 48, 48, 48, 28, 1, 1, 1, 1, 8, 11, 28, 28, 28, 28, 28, 28, 48, 48, 28, 28, 1, 1] 48
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 170
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057951 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCN(CC(F)(F)F)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 27, 28, 25, 28, 28, 25, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 28, 28, 28, 28, 25, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 28, 28] 48
rigid atoms, others: [32, 33, 34, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 35, 36, 39, 40])
total number of confs: 99
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057951 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057951
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057951/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057951
Building REAL300000057952
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057952'
/scratch/stefan/7769638/working/building/REAL300000057952 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057952

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057952/0 /scratch/stefan/7769638/working/building/REAL300000057952 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 991)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/991
`/scratch/stefan/7769638/working/3D/991' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C2SC=C3)C=C1)

`REAL300000057952.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057952/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057952 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C2SC=C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 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, 8, 15, 15, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 8, 15, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 46
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057952 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCCC3=C2SC=C3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 17, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 18
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 22, 23, 24, 25, 26, 36])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057952 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057952
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057952/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057952
Building REAL300000057953
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057953'
/scratch/stefan/7769638/working/building/REAL300000057953 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057953

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057953/0 /scratch/stefan/7769638/working/building/REAL300000057953 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 992)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/992
`/scratch/stefan/7769638/working/3D/992' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Cl)C=C1F)

`REAL300000057953.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057953/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057953 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 49, 49, 40, 49, 49, 49, 49, 33, 33, 33, 14, 7, 1, 1, 1, 1, 49, 49, 49] 49
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 140
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057953 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [10, 1, 10, 10, 25, 25, 25, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 25, 49, 49, 49, 49, 49, 1, 1, 1] 49
rigid atoms, others: [1, 34, 35, 33, 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])
total number of confs: 145
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057953 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057953
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057953/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057953
Building REAL300000057954
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057954'
/scratch/stefan/7769638/working/building/REAL300000057954 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057954

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057954/0 /scratch/stefan/7769638/working/building/REAL300000057954 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 993)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/993
`/scratch/stefan/7769638/working/3D/993' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1C(C)CCCC1(C)C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057954.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057954.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057954/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057954 none CC(CCC1C(C)CCCC1(C)C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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, 5, 5, 5, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [14, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 26, 26, 26, 44, 44, 44, 44, 44, 44, 44, 44, 44, 14, 14, 14, 3, 3, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 26, 44, 44, 44, 44, 44] 44
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 39, 44, 12, 11, 40, 35, 43, 41, 42] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56])
total number of confs: 159
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057954 none CC(CCC1C(C)CCCC1(C)C)=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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, 5, 5, 5, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 13, 13, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 3, 1, 1, 1, 1] 44
rigid atoms, others: [22, 17, 18, 19, 20, 53, 54, 55, 56, 25, 26, 21] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 157
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057954 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057954
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057954/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057954
Building REAL300000057955
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057955'
/scratch/stefan/7769638/working/building/REAL300000057955 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057955

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057955/0 /scratch/stefan/7769638/working/building/REAL300000057955 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 994)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/994
`/scratch/stefan/7769638/working/3D/994' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=NN1C)

`REAL300000057955.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057955.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057955/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057955 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 38, 38, 38, 38, 38, 38, 38, 38, 38, 28, 28, 28, 16, 7, 1, 1, 1, 1, 38, 38, 38, 38] 38
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 80
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057955 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [10, 1, 10, 10, 24, 24, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 10, 10, 10, 24, 38, 38, 38, 38, 38, 1, 2, 2, 2] 38
rigid atoms, others: [1, 35, 16, 17, 18, 19, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38])
total number of confs: 117
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057955 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057955
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057955/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057955
Building REAL300000057956
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057956'
/scratch/stefan/7769638/working/building/REAL300000057956 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057956

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057956/0 /scratch/stefan/7769638/working/building/REAL300000057956 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 995)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/995
`/scratch/stefan/7769638/working/3D/995' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CNC2=CC(C)=NN2C1=O)

`REAL300000057956.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057956.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057956/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057956 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CNC2=CC(C)=NN2C1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 11, 7, 7, 7, 6, 6, 7, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 14, 7, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41] 41
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 82
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057956 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CNC2=CC(C)=NN2C1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 11, 7, 7, 7, 6, 6, 7, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 1, 7, 7, 23, 23, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 41, 41, 41, 41, 41, 1, 1, 1, 2, 2, 2] 41
rigid atoms, others: [1, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41])
total number of confs: 119
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057956 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057956
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057956/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057956
Building REAL300000057957
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057957'
/scratch/stefan/7769638/working/building/REAL300000057957 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057957

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057957/0 /scratch/stefan/7769638/working/building/REAL300000057957 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 996)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/996
`/scratch/stefan/7769638/working/3D/996' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1)

`REAL300000057957.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057957.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057957/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057957 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [33, 33, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 33, 92, 92, 92, 92, 92, 92, 130, 130, 130, 33, 33, 33, 13, 7, 1, 1, 1, 1, 92, 92, 92, 92, 130, 130, 130, 130, 130, 130, 130] 130
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 297
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057957 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 1, 12, 12, 41, 41, 41, 84, 92, 92, 89, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 41, 84, 92, 92, 92, 92, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7] 130
rigid atoms, others: [1, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 283
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057957 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [36, 7, 36, 36, 78, 78, 78, 130, 130, 130, 130, 130, 130, 130, 130, 130, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 36, 36, 36, 78, 130, 130, 130, 130, 130, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1] 130
rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 352
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057957 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057957
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057957/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057957
Building REAL300000057958
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057958'
/scratch/stefan/7769638/working/building/REAL300000057958 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057958

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057958/0 /scratch/stefan/7769638/working/building/REAL300000057958 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 997)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/997
`/scratch/stefan/7769638/working/3D/997' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1)

`REAL300000057958.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057958.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057958/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057958 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 86, 86, 86, 86, 86, 86, 109, 109, 109, 109, 109, 30, 30, 30, 14, 7, 1, 1, 1, 1, 86, 86, 86, 86, 109, 109, 109, 109, 109, 109, 109, 109, 109] 109
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 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: 224
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057958 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 35, 36, 36, 82, 86, 86, 85, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 10, 35, 82, 86, 86, 86, 86, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 109
rigid atoms, others: [1, 37, 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, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 264
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057958 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 6, 26, 26, 58, 58, 58, 107, 109, 109, 109, 109, 109, 109, 109, 109, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 58, 107, 109, 109, 109, 109, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 109
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 309
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057958 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057958
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057958/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057958
Building REAL300000057959
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057959'
/scratch/stefan/7769638/working/building/REAL300000057959 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057959

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057959/0 /scratch/stefan/7769638/working/building/REAL300000057959 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 998)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/998
`/scratch/stefan/7769638/working/3D/998' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(NC(=O)C(C)(C)C)C=N1)

`REAL300000057959.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057959.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057959/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057959 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(NC(=O)C(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 6, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 9
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 31
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057959 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(NC(=O)C(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 6, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 1, 5, 5, 5, 5, 5, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 9
rigid atoms, others: [0, 1, 2, 3, 4, 49, 38, 32, 16, 17, 18, 19, 20, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 25
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057959 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057959
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057959/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057959
Building REAL300000057960
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057960'
/scratch/stefan/7769638/working/building/REAL300000057960 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057960

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057960/0 /scratch/stefan/7769638/working/building/REAL300000057960 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 999)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/999
`/scratch/stefan/7769638/working/3D/999' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Cl)C=C1O)

`REAL300000057960.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057960.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057960/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057960 none COC(=O)C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Cl)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 8, 8, 21, 21, 21, 43, 47, 47, 46, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 10, 10, 10, 1, 8, 21, 43, 47, 47, 47, 47, 1, 2] 154
rigid atoms, others: [2, 4, 5, 6, 7, 22, 23, 24, 25, 26, 38, 30] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 39])
total number of confs: 143
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057960 none COC(=O)C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=C(Cl)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [77, 77, 47, 77, 47, 47, 27, 27, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 47, 47, 47, 47, 47, 77, 77, 77, 47, 27, 12, 7, 1, 1, 1, 1, 47, 94] 154
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 278
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057960 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057960
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057960/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057960
Building REAL300000057961
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057961'
/scratch/stefan/7769638/working/building/REAL300000057961 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057961

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057961/0 /scratch/stefan/7769638/working/building/REAL300000057961 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1000)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1000
`/scratch/stefan/7769638/working/3D/1000' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=C(COCC3)S2)C=C1)

`REAL300000057961.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057961.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057961/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057961 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=C(COCC3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 5, 12, 5, 5, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 4, 6, 6, 6, 22, 22, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 4, 6, 22, 31, 31, 31, 31, 31, 31, 1, 1] 31
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: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057961 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=C(COCC3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 5, 12, 5, 5, 14, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 14, 6, 1, 1, 1, 1, 1, 1, 36, 36] 36
rigid atoms, others: [32, 33, 34, 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, 35, 22, 23, 24, 25, 26, 27, 28, 36])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057961 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057961
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057961/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057961
Building REAL300000057962
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057962'
/scratch/stefan/7769638/working/building/REAL300000057962 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057962

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057962/0 /scratch/stefan/7769638/working/building/REAL300000057962 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1001)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1001
`/scratch/stefan/7769638/working/3D/1001' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNN=C2C2=CC=CC(F)=C2)C=C1)

`REAL300000057962.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057962/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057962 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNN=C2C2=CC=CC(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 10, 10, 36, 36, 94, 94, 94, 94, 94, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 8, 10, 36, 94, 94, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 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])
total number of confs: 306
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057962 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNN=C2C2=CC=CC(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 88, 94, 88, 94, 94, 83, 36, 36, 36, 13, 13, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 94, 94, 94, 94, 83, 36, 13, 1, 1, 11, 11, 11, 11, 94, 94] 201
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057962 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CNN=C2C2=CC=CC(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 99, 99, 99, 43, 43, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 99, 43, 11, 11, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 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, 38, 39])
total number of confs: 574
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057962 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057962
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057962/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057962
Building REAL300000057963
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057963'
/scratch/stefan/7769638/working/building/REAL300000057963 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057963

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057963/0 /scratch/stefan/7769638/working/building/REAL300000057963 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1002)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1002
`/scratch/stefan/7769638/working/3D/1002' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(CCCC3)O2)C=C1)

`REAL300000057963.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057963.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057963/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057963 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(CCCC3)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 8, 8, 8, 25, 25, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 6, 8, 25, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1] 34
rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057963 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=C(CCCC3)O2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 35, 15, 14, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 35
rigid atoms, others: [32, 33, 34, 35, 36, 37, 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, 38, 22, 23, 24, 25, 26, 27, 28, 39])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057963 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057963
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057963/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057963
Building REAL300000057964
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057964'
/scratch/stefan/7769638/working/building/REAL300000057964 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057964

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057964/0 /scratch/stefan/7769638/working/building/REAL300000057964 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1003)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1003
`/scratch/stefan/7769638/working/3D/1003' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC(F)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057964.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057964.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057964/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057964 none COC(=O)C1=CC(F)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 1, 1, 1, 4, 8, 15, 15, 15, 15, 15] 21
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 3, 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: 59
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057964 none COC(=O)C1=CC(F)=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 15, 21, 15, 15, 15, 15, 15, 15, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 15, 15, 15, 9, 5, 5, 1, 1, 1, 1] 21
rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 52
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057964 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057964
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057964/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057964
Building REAL300000057965
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057965'
/scratch/stefan/7769638/working/building/REAL300000057965 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057965

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057965/0 /scratch/stefan/7769638/working/building/REAL300000057965 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1004)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1004
`/scratch/stefan/7769638/working/3D/1004' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(Cl)N(C3=CC=CC=C3)N=C2)C=C1)

`REAL300000057965.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057965.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057965/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057965 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(Cl)N(C3=CC=CC=C3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 5, 1, 1] 7
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 39, 25, 26, 27, 28] set([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: 15
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057965 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(Cl)N(C3=CC=CC=C3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [70, 67, 70, 67, 70, 70, 67, 29, 28, 29, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 1, 1, 70, 70, 70, 70, 67, 28, 8, 5, 5, 3, 5, 5, 1, 70, 70] 89
rigid atoms, others: [37, 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, 38, 39])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057965 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(Cl)N(C3=CC=CC=C3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.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, 8, 1, 11, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 89, 89, 89, 89, 50, 50, 50, 24, 24, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 89, 89, 89, 89, 89, 50, 24, 1, 1, 1, 1, 1, 5, 89, 89] 89
rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 250
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057965 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057965
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057965/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057965
Building REAL300000057966
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057966'
/scratch/stefan/7769638/working/building/REAL300000057966 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057966

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057966/0 /scratch/stefan/7769638/working/building/REAL300000057966 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1005)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1005
`/scratch/stefan/7769638/working/3D/1005' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)N1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057966.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057966.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057966/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057966 none CCC(C)N1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 31, 32, 32, 63, 69, 69, 64, 65, 69, 69, 69, 69, 10, 10, 10, 10, 10, 5, 6, 6, 6, 1, 1, 8, 31, 63, 69, 69, 69, 69] 90
rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 34] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 272
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057966 none CCC(C)N1N=CC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 69, 90, 69, 69, 69, 69, 23, 23, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 90, 90, 90, 90, 90, 90, 90, 90, 90, 69, 69, 23, 11, 7, 1, 1, 1, 1] 90
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 228
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057966 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057966
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057966/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057966
Building REAL300000057967
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057967'
/scratch/stefan/7769638/working/building/REAL300000057967 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057967

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057967/0 /scratch/stefan/7769638/working/building/REAL300000057967 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1006)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1006
`/scratch/stefan/7769638/working/3D/1006' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC([N+](=O)[O-])=C2)C=C1)

`REAL300000057967.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057967.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057967/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057967 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 1, 1, 7, 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, 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, 1, 1, 1, 1, 10, 19, 19, 19, 35, 35, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 10, 19, 35, 62, 62, 62, 1, 1] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 23, 24, 25, 26] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057967 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC(F)=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 32, 32, 32, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 32, 12, 1, 1, 1, 63, 63] 63
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 33, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057967 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057967
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057967/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057967
Building REAL300000057968
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057968'
/scratch/stefan/7769638/working/building/REAL300000057968 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057968

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057968/0 /scratch/stefan/7769638/working/building/REAL300000057968 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1007)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1007
`/scratch/stefan/7769638/working/3D/1007' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCCCC3)N=C2)C=C1)

`REAL300000057968.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057968/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057968 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCCCC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 17, 17, 51, 51, 92, 92, 92, 201, 201, 201, 201, 201, 92, 92, 1, 1, 1, 1, 8, 17, 51, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 92, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 479
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057968 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCCCC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 92, 92, 87, 92, 92, 79, 31, 30, 31, 8, 8, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 92, 92, 92, 92, 79, 30, 8, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 92, 92] 201
rigid atoms, others: [43, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45])
total number of confs: 286
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057968 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CN(C3CCCCC3)N=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 192, 114, 114, 114, 60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 201, 192, 114, 60, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 43, 44, 45])
total number of confs: 564
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057968 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057968
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057968/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057968
Building REAL300000057969
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057969'
/scratch/stefan/7769638/working/building/REAL300000057969 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057969

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057969/0 /scratch/stefan/7769638/working/building/REAL300000057969 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1008)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1008
`/scratch/stefan/7769638/working/3D/1008' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C2C(=C1)CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057969.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057969.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057969/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057969 none N#CC1=CC=C2C(=C1)CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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: [8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 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, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 47
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057969 none N#CC1=CC=C2C(=C1)CCC2=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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: [8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 18, 18, 18, 18, 13, 7, 1, 1, 1, 1] 18
rigid atoms, others: [34, 35, 36, 37, 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])
total number of confs: 49
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057969 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057969
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057969/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057969
Building REAL300000057970
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057970'
/scratch/stefan/7769638/working/building/REAL300000057970 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057970

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057970/0 /scratch/stefan/7769638/working/building/REAL300000057970 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1009)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1009
`/scratch/stefan/7769638/working/3D/1009' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(F)C=C(Br)C=C2F)C=C1)

`REAL300000057970.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057970.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057970/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057970 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(F)C=C(Br)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 15, 1, 1, 17, 1, 1, 15, 1, 1, 7, 7, 6, 6, 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, 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, 8, 17, 17, 17, 32, 32, 42, 42, 42, 32, 32, 42, 42, 42, 1, 1, 1, 1, 8, 17, 32, 42, 42, 1, 1] 42
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 119
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057970 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=C(F)C=C(Br)C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 11, 8, 8, 1, 1, 1, 15, 1, 1, 17, 1, 1, 15, 1, 1, 7, 7, 6, 6, 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, 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, 23, 22, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 22, 7, 1, 1, 44, 44] 44
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057970 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057970
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057970/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057970
Building REAL300000057971
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057971'
/scratch/stefan/7769638/working/building/REAL300000057971 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057971

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057971/0 /scratch/stefan/7769638/working/building/REAL300000057971 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1010)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1010
`/scratch/stefan/7769638/working/3D/1010' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCCCC3C2)C=C1)

`REAL300000057971.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057971.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057971/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057971 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCCCC3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 16, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 11, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057971 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC3CCCCC3C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 27
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, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 41, 21, 22, 23, 24, 25, 26, 42])
total number of confs: 69
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057971 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057971
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057971/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057971
Building REAL300000057972
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057972'
/scratch/stefan/7769638/working/building/REAL300000057972 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057972

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057972/0 /scratch/stefan/7769638/working/building/REAL300000057972 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1011)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1011
`/scratch/stefan/7769638/working/3D/1011' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CCO)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1)

`REAL300000057972.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057972.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057972/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057972 none CN(CCO)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 29, 41, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 45, 59, 59, 45, 45, 59, 59, 59, 59, 1, 1, 10, 10, 10, 29, 29, 41, 41, 123, 1, 1, 6, 20, 45, 59, 59, 59, 59, 1] 603
rigid atoms, others: [1, 34, 35, 5, 6, 7, 8, 9, 43, 24, 25] set([0, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 545
number of broken/clashed sets: 98
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057972 none CN(CCO)C1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [153, 59, 153, 201, 201, 59, 59, 59, 20, 20, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 59, 59, 153, 153, 153, 201, 201, 201, 201, 603, 59, 59, 20, 8, 6, 1, 1, 1, 1, 59] 603
rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 1218
number of broken/clashed sets: 98
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057972 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057972
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057972/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057972
Building REAL300000057973
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057973'
/scratch/stefan/7769638/working/building/REAL300000057973 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057973

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057973/0 /scratch/stefan/7769638/working/building/REAL300000057973 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1012)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1012
`/scratch/stefan/7769638/working/3D/1012' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C2=CC=CC=C2)C=C1)

`REAL300000057973.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057973/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057973 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 26, 12, 7, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34] 34
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 66
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057973 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 13, 14, 14, 32, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 10, 10, 10, 13, 32, 34, 34, 34, 34, 3, 3, 1, 3, 3, 1, 1] 34
rigid atoms, others: [1, 41, 42, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057973 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 3, 11, 11, 15, 16, 16, 32, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 16, 32, 34, 34, 34, 34, 1, 1, 1, 1, 1, 3, 3] 34
rigid atoms, others: [36, 37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42])
total number of confs: 92
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057973 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057973
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057973/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057973
Building REAL300000057974
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057974'
/scratch/stefan/7769638/working/building/REAL300000057974 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057974

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057974/0 /scratch/stefan/7769638/working/building/REAL300000057974 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1013)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1013
`/scratch/stefan/7769638/working/3D/1013' -> `0.mol2'
Preparing input files

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

`REAL300000057974.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057974.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057974/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057974 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 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
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 5, 1, 1, 1, 1, 9, 9, 9, 9] 9
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057974 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 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
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 4, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 9, 9, 9, 9, 9, 1, 1, 1, 1] 9
rigid atoms, others: [1, 37, 38, 39, 40, 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])
total number of confs: 33
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057974 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057974
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057974/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057974
Building REAL300000057975
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057975'
/scratch/stefan/7769638/working/building/REAL300000057975 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057975

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057975/0 /scratch/stefan/7769638/working/building/REAL300000057975 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1014)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1014
`/scratch/stefan/7769638/working/3D/1014' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CC=C1C(C)(C)C)

`REAL300000057975.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057975.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057975/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057975 none COC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CC=C1C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'C.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, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 1, 5, 5, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 5, 12, 36, 36, 36, 36, 36, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 36
rigid atoms, others: [1, 2, 3, 4, 37, 38, 39, 19, 20, 21, 22, 23] set([0, 5, 6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 104
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057975 none COC1=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=CC=C1C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'C.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, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 25, 25, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 25, 15, 7, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 36
rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 78
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057975 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057975
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057975/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057975
Building REAL300000057976
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057976'
/scratch/stefan/7769638/working/building/REAL300000057976 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057976

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057976/0 /scratch/stefan/7769638/working/building/REAL300000057976 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1015)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1015
`/scratch/stefan/7769638/working/3D/1015' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCS1(=O)=O)

`REAL300000057976.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057976.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057976/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057976 none CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCS1(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 8, 25, 25, 25, 25, 25, 1, 1, 1, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 38, 18, 19, 20, 21, 22, 36, 26, 27, 28, 37] set([32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 29, 30, 31])
total number of confs: 67
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057976 none CC1CC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CCS1(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 14, 7, 1, 1, 1, 1, 25, 25, 25, 25] 25
rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38])
total number of confs: 55
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057976 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057976
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057976/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057976
Building REAL300000057977
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057977'
/scratch/stefan/7769638/working/building/REAL300000057977 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057977

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057977/0 /scratch/stefan/7769638/working/building/REAL300000057977 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1016)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1016
`/scratch/stefan/7769638/working/3D/1016' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(Br)N=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057977.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057977.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057977/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057977 none CN1C=C(Br)N=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 1, 17, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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, 5, 5, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 5, 9, 24, 24, 24, 24, 24] 24
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])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057977 none CN1C=C(Br)N=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 1, 17, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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, 22, 22, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 22, 8, 5, 1, 1, 1, 1] 24
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, 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
/scratch/stefan/7769638/working/building/REAL300000057977 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057977
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057977/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057977
Building REAL300000057978
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057978'
/scratch/stefan/7769638/working/building/REAL300000057978 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057978

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057978/0 /scratch/stefan/7769638/working/building/REAL300000057978 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1017)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1017
`/scratch/stefan/7769638/working/3D/1017' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1)

`REAL300000057978.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057978.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057978/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057978 none COC1=CC(C)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 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, 7, 4, 7, 6, 4, 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
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 19, 19, 19, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 2, 2, 2, 1, 2, 2, 2, 10, 19, 45, 45, 45, 45, 45, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 22, 23, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 137
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057978 none COC1=CC(C)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 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, 7, 4, 7, 6, 4, 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
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 24, 24, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 24, 12, 7, 1, 1, 1, 1, 45] 45
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 88
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057978 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057978
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057978/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057978
Building REAL300000057979
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057979'
/scratch/stefan/7769638/working/building/REAL300000057979 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057979

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057979/0 /scratch/stefan/7769638/working/building/REAL300000057979 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1018)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1018
`/scratch/stefan/7769638/working/3D/1018' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1O)

`REAL300000057979.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057979.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057979/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057979 none COC1=CC(C)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7]
1  hydrogens need rotated
208  conformations in input
total number of sets (complete confs): 208
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 38, 38, 38, 98, 104, 104, 100, 104, 104, 104, 104, 104, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 10, 38, 98, 104, 104, 104, 104, 1, 2] 208
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40])
total number of confs: 307
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057979 none COC1=CC(C)=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7]
1  hydrogens need rotated
208  conformations in input
total number of sets (complete confs): 208
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 104, 104, 104, 46, 46, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 46, 18, 7, 1, 1, 1, 1, 104, 208] 208
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 379
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057979 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057979
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057979/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057979
Building REAL300000057980
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057980'
/scratch/stefan/7769638/working/building/REAL300000057980 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057980

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057980/0 /scratch/stefan/7769638/working/building/REAL300000057980 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1019)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1019
`/scratch/stefan/7769638/working/3D/1019' -> `0.mol2'
Preparing input files

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

`REAL300000057980.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057980.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057980/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057980 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C(C)S(C)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 14, 5, 11, 11, 7, 7, 7, 6, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 7, 7, 6, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 16, 16, 23, 23, 23, 11, 11, 11, 7, 6, 1, 1, 1, 1, 16, 16, 16, 16, 23, 23, 23] 23
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 91
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057980 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057980
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057980/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057980
Building REAL300000057981
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057981'
/scratch/stefan/7769638/working/building/REAL300000057981 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057981

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057981/0 /scratch/stefan/7769638/working/building/REAL300000057981 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1020)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1020
`/scratch/stefan/7769638/working/3D/1020' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=CC=CC=C3S2)C=C1)

`REAL300000057981.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057981.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057981/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057981 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=CC=CC=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 6, 6, 7, 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, 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, 4, 6, 6, 6, 22, 22, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 4, 6, 22, 33, 33, 33, 33, 1, 1] 33
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: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057981 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=NC3=CC=CC=C3S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 6, 6, 7, 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, 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, 37, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 15, 7, 1, 1, 1, 1, 37, 37] 37
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, 34, 33, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057981 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057981
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057981/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057981
Building REAL300000057982
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057982'
/scratch/stefan/7769638/working/building/REAL300000057982 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057982

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057982/0 /scratch/stefan/7769638/working/building/REAL300000057982 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1021)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1021
`/scratch/stefan/7769638/working/3D/1021' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1(C2=CC=CN=C2)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1)

`REAL300000057982.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057982/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057982 none N#CC1(C2=CC=CN=C2)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 9, 9, 9, 45, 63, 63, 50, 50, 63, 63, 63, 63, 1, 1, 13, 13, 12, 13, 1, 1, 1, 1, 9, 45, 63, 63, 63, 63, 1, 1, 1, 1] 117
rigid atoms, others: [0, 1, 2, 3, 33, 32, 9, 10, 11, 12, 34, 13, 43, 44, 35, 45, 26, 27, 42] set([4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 245
number of broken/clashed sets: 68
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057982 none N#CC1(C2=CC=CN=C2)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 61, 61, 61, 117, 117, 117, 117, 117, 117, 117, 117, 117, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13, 61, 117, 117, 117, 117, 117, 13, 13, 13, 13] 117
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 321
number of broken/clashed sets: 68
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057982 none N#CC1(C2=CC=CN=C2)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 117, 117, 117, 117, 117, 63, 63, 63, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 117, 117, 117, 117, 63, 63, 63, 63, 16, 7, 1, 1, 1, 1, 63, 63, 63, 63] 117
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, 42, 43, 44, 45])
total number of confs: 202
number of broken/clashed sets: 68
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057982 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057982
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057982/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057982
Building REAL300000057983
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057983'
/scratch/stefan/7769638/working/building/REAL300000057983 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057983

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057983/0 /scratch/stefan/7769638/working/building/REAL300000057983 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1022)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1022
`/scratch/stefan/7769638/working/3D/1022' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=C(F)C=C3NC2=O)C=C1)

`REAL300000057983.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057983.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057983/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057983 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=C(F)C=C3NC2=O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 1, 1] 7
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 25, 26, 27, 28, 37] set([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])
total number of confs: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057983 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=CC=C(F)C=C3NC2=O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 16, 8, 1, 1, 1, 1, 1, 34, 34] 34
rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 37, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057983 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057983
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057983/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057983
Building REAL300000057984
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057984'
/scratch/stefan/7769638/working/building/REAL300000057984 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057984

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057984/0 /scratch/stefan/7769638/working/building/REAL300000057984 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1023)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1023
`/scratch/stefan/7769638/working/3D/1023' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21)

`REAL300000057984.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057984/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057984 none CN1C(=O)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 8, 18, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 18, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1] 34
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 40, 41, 20, 21, 22, 23, 24, 25, 26, 37] set([6, 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: 95
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057984 none CN1C(=O)C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 28, 28, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 28, 12, 7, 1, 1, 1, 1, 34, 34, 34, 34, 34] 34
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41])
total number of confs: 67
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057984 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057984
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057984/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057984
Building REAL300000057985
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057985'
/scratch/stefan/7769638/working/building/REAL300000057985 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057985

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057985/0 /scratch/stefan/7769638/working/building/REAL300000057985 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1024)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1024
`/scratch/stefan/7769638/working/3D/1024' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C2=C1C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CCC2)

`REAL300000057985.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057985/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057985 none CC1=NN(C)C2=C1C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 8, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 39, 40, 41, 22, 23, 24, 38, 37] 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])
total number of confs: 55
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057985 none CC1=NN(C)C2=C1C(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 7, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17] 17
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 45
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057985 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057985
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057985/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057985
Building REAL300000057986
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057986'
/scratch/stefan/7769638/working/building/REAL300000057986 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057986

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057986/0 /scratch/stefan/7769638/working/building/REAL300000057986 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1025)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1025
`/scratch/stefan/7769638/working/3D/1025' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1F)

`REAL300000057986.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057986.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057986/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057986 none COC(=O)C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 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]
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: [12, 12, 1, 12, 1, 1, 1, 1, 11, 11, 27, 27, 27, 49, 55, 55, 52, 52, 55, 55, 55, 55, 1, 1, 1, 1, 12, 12, 12, 1, 11, 27, 49, 55, 55, 55, 55, 1, 1] 88
rigid atoms, others: [2, 4, 5, 6, 7, 22, 23, 24, 25, 38, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 189
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057986 none COC(=O)C1=CC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 55, 88, 55, 55, 26, 26, 8, 8, 6, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 55, 55, 55, 55, 88, 88, 88, 55, 26, 8, 6, 1, 1, 1, 1, 55, 55] 88
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 200
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057986 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057986
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057986/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057986
Building REAL300000057987
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057987'
/scratch/stefan/7769638/working/building/REAL300000057987 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057987

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057987/0 /scratch/stefan/7769638/working/building/REAL300000057987 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1026)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1026
`/scratch/stefan/7769638/working/3D/1026' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1COC2=CC=CC=C2C1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057987.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057987/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057987 none CC1COC2=CC=CC=C2C1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 18, 18, 18, 18, 18] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 32, 33, 28, 29, 30, 31] set([35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 49
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057987 none CC1COC2=CC=CC=C2C1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 7, 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: 42
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057987 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057987
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057987/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057987
Building REAL300000057988
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057988'
/scratch/stefan/7769638/working/building/REAL300000057988 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057988

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057988/0 /scratch/stefan/7769638/working/building/REAL300000057988 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1027)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1027
`/scratch/stefan/7769638/working/3D/1027' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3CCOCC3)C2)C=C1)

`REAL300000057988.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057988.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057988/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057988 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3CCOCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 10, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1] 29
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 43, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057988 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3CCOCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 28, 10, 9, 10, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 29, 29, 29, 29, 28, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 29, 29] 29
rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057988 none O=C([O-])C1=CC=C(NC(=O)NN=C2CC(C3CCOCC3)C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 28, 11, 11, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 29, 29, 29, 29, 28, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 29, 29] 29
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43])
total number of confs: 75
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057988 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057988
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057988/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057988
Building REAL300000057989
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057989'
/scratch/stefan/7769638/working/building/REAL300000057989 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057989

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057989/0 /scratch/stefan/7769638/working/building/REAL300000057989 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1028)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1028
`/scratch/stefan/7769638/working/3D/1028' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1C)

`REAL300000057989.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057989/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057989 none COC1=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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]
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, 6, 6, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 2, 2, 2, 6, 10, 22, 22, 22, 22, 22, 1, 1, 2, 2, 2] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 35, 20, 21, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057989 none COC1=NC(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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]
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, 20, 20, 10, 10, 7, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 22, 22, 22, 22, 22, 22, 22, 20, 10, 7, 1, 1, 1, 1, 22, 22, 22, 22, 22] 22
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 48
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057989 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057989
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057989/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057989
Building REAL300000057990
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057990'
/scratch/stefan/7769638/working/building/REAL300000057990 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057990

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057990/0 /scratch/stefan/7769638/working/building/REAL300000057990 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1029)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1029
`/scratch/stefan/7769638/working/3D/1029' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C2CC2)C=NN1C)

`REAL300000057990.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057990.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057990/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057990 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C2CC2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [35, 35, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 35, 68, 68, 85, 85, 68, 68, 68, 68, 35, 35, 35, 15, 7, 1, 1, 1, 1, 85, 85, 85, 85, 85, 68, 68, 68, 68] 85
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 192
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057990 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C2CC2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [8, 1, 8, 8, 23, 24, 24, 58, 68, 68, 58, 58, 68, 68, 68, 68, 1, 1, 1, 7, 7, 1, 1, 1, 1, 9, 9, 9, 23, 58, 68, 68, 68, 68, 7, 7, 7, 7, 7, 1, 2, 2, 2] 85
rigid atoms, others: [1, 39, 16, 17, 18, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42])
total number of confs: 272
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057990 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=C(C2CC2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [31, 7, 31, 31, 52, 53, 53, 84, 85, 85, 84, 84, 85, 85, 85, 85, 7, 1, 1, 1, 1, 7, 7, 7, 7, 32, 32, 32, 52, 84, 85, 85, 85, 85, 1, 1, 1, 1, 1, 7, 8, 8, 8] 85
rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 251
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057990 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057990
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057990/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057990
Building REAL300000057991
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057991'
/scratch/stefan/7769638/working/building/REAL300000057991 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057991

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057991/0 /scratch/stefan/7769638/working/building/REAL300000057991 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1030)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1030
`/scratch/stefan/7769638/working/3D/1030' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=NOC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057991.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057991.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057991/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057991 none COCC1=NOC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 5, 1, 8, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [19, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 21, 21, 37, 43, 43, 37, 41, 43, 43, 43, 43, 19, 19, 19, 8, 8, 1, 8, 20, 37, 43, 43, 43, 43] 60
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28] set([0, 1, 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])
total number of confs: 185
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057991 none COCC1=NOC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 12, 5, 1, 8, 12, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 43, 43, 43, 43, 43, 16, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 43, 16, 6, 6, 1, 1, 1, 1] 60
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])
total number of confs: 157
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057991 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057991
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057991/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057991
Building REAL300000057992
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057992'
/scratch/stefan/7769638/working/building/REAL300000057992 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057992

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057992/0 /scratch/stefan/7769638/working/building/REAL300000057992 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1031)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1031
`/scratch/stefan/7769638/working/3D/1031' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CCOCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057992.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057992.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057992/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057992 none CCC1CCOCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 24, 25, 25, 24, 24, 25, 25, 25, 25, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 24, 25, 25, 25, 25] 27
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 27, 28, 29, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39])
total number of confs: 80
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057992 none CCC1CCOCC1=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 25, 25, 25, 25, 25, 25, 25, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 27, 25, 25, 25, 25, 25, 25, 25, 13, 7, 1, 1, 1, 1] 27
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 70
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057992 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057992
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057992/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057992
Building REAL300000057993
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057993'
/scratch/stefan/7769638/working/building/REAL300000057993 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057993

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057993/0 /scratch/stefan/7769638/working/building/REAL300000057993 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1032)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1032
`/scratch/stefan/7769638/working/3D/1032' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1C=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)

`REAL300000057993.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057993.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057993/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057993 none CCCN1C=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 72, 82, 82, 72, 75, 82, 82, 82, 82, 12, 12, 12, 12, 12, 6, 6, 1, 1, 9, 29, 72, 82, 82, 82, 82] 137
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 326
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057993 none CCCN1C=NC=C1C=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [137, 137, 82, 82, 82, 82, 82, 36, 36, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 137, 137, 82, 82, 36, 16, 7, 1, 1, 1, 1] 137
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 443
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057993 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057993
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057993/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057993
Building REAL300000057994
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057994'
/scratch/stefan/7769638/working/building/REAL300000057994 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057994

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057994/0 /scratch/stefan/7769638/working/building/REAL300000057994 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1033)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1033
`/scratch/stefan/7769638/working/3D/1033' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC(Cl)=C(Cl)C=C32)C=C1)

`REAL300000057994.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057994.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057994/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057994 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC(Cl)=C(Cl)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 12, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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
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, 8, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 8, 12, 19, 19, 19, 19, 19, 19, 1, 1] 19
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: 46
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057994 none O=C([O-])C1=CC=C(NC(=O)NN=C2CCOC3=CC(Cl)=C(Cl)C=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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, 8, 1, 11, 8, 8, 1, 5, 5, 12, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 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, 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
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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 19, 19] 19
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 37, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 49
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057994 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057994
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057994/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057994
Building REAL300000057995
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057995'
/scratch/stefan/7769638/working/building/REAL300000057995 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057995

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057995/0 /scratch/stefan/7769638/working/building/REAL300000057995 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1034)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1034
`/scratch/stefan/7769638/working/3D/1034' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=NSN=C3C=C2)C=C1)

`REAL300000057995.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057995.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057995/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057995 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=NSN=C3C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 14, 8, 1, 1, 1, 1, 1, 7, 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, 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, 10, 12, 12, 12, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 10, 12, 29, 46, 46, 46, 1, 1] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057995 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC3=NSN=C3C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', '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, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 8, 14, 8, 1, 1, 1, 1, 1, 7, 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, 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, 23, 22, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 22, 6, 1, 1, 1, 47, 47] 47
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, 33, 32, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 129
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057995 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057995
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057995/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057995
Building REAL300000057996
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057996'
/scratch/stefan/7769638/working/building/REAL300000057996 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057996

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057996/0 /scratch/stefan/7769638/working/building/REAL300000057996 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1035)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1035
`/scratch/stefan/7769638/working/3D/1035' -> `0.mol2'
Preparing input files

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

`REAL300000057996.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057996.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057996/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057996 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 75, 75, 75, 75, 75, 75, 75, 27, 27, 27, 15, 7, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75] 75
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 125
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057996 none CC(=NNC(=O)NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 41, 41, 41, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 41, 75, 75, 75, 75, 75, 1, 2, 2, 2, 1, 1] 75
rigid atoms, others: [1, 37, 38, 33, 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, 34, 35, 36])
total number of confs: 213
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057996 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057996
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057996/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057996
Building REAL300000057997
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057997'
/scratch/stefan/7769638/working/building/REAL300000057997 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057997

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057997/0 /scratch/stefan/7769638/working/building/REAL300000057997 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1036)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1036
`/scratch/stefan/7769638/working/3D/1036' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)O1)

`REAL300000057997.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057997.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057997/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057997 none O=C([O-])CCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', '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']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 4, 7, 6, 4, 7, 7, 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
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [29, 17, 21, 9, 1, 1, 1, 1, 1, 1, 6, 6, 24, 25, 25, 57, 72, 72, 57, 57, 72, 72, 72, 72, 1, 17, 17, 9, 9, 1, 1, 6, 24, 57, 72, 72, 72, 72] 168
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])
total number of confs: 386
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057997 none O=C([O-])CCC1=CC=C(C=NNC(=O)NC2=CC=C(C(=O)[O-])C=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', 'N.am', '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']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 4, 7, 6, 4, 7, 7, 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
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [168, 168, 161, 144, 72, 72, 72, 72, 38, 38, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 168, 168, 144, 144, 72, 72, 38, 16, 7, 1, 1, 1, 1] 168
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: 601
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057997 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057997
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057997/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057997
Building REAL300000057998
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057998'
/scratch/stefan/7769638/working/building/REAL300000057998 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057998

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057998/0 /scratch/stefan/7769638/working/building/REAL300000057998 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1037)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1037
`/scratch/stefan/7769638/working/3D/1037' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC2=C(C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)N2)S1)

`REAL300000057998.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057998.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057998/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057998 none CC1=CC2=C(C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)N2)S1 NO_LONG_NAME
dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 6, 6, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 2, 2, 2, 1, 1, 6, 14, 32, 32, 32, 32, 32, 1] 32
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 36, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 90
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057998 none CC1=CC2=C(C=C(C=NNC(=O)NC3=CC=C(C(=O)[O-])C=C3)N2)S1 NO_LONG_NAME
dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 23, 23, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 32, 23, 8, 5, 1, 1, 1, 1, 32] 32
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 62
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057998 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057998
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057998/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057998
Building REAL300000057999
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000057999'
/scratch/stefan/7769638/working/building/REAL300000057999 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000057999

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000057999/0 /scratch/stefan/7769638/working/building/REAL300000057999 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1038)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1038
`/scratch/stefan/7769638/working/3D/1038' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC2=CC=CC=C21)

`REAL300000057999.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000057999.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000057999/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057999 none CC1(C)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 8, 8, 19, 20, 20, 19, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 19, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 68
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000057999 none CC1(C)CCC(=NNC(=O)NC2=CC=C(C(=O)[O-])C=C2)CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 12, 12, 7, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 7, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20] 20
rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48])
total number of confs: 49
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000057999 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000057999
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000057999/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000057999
Building REAL300000058000
mkdir: created directory `/scratch/stefan/7769638/working/building/REAL300000058000'
/scratch/stefan/7769638/working/building/REAL300000058000 /scratch/stefan/7769638/working /scratch/stefan/7769638
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000058000

mkdir: created directory `0'
/scratch/stefan/7769638/working/building/REAL300000058000/0 /scratch/stefan/7769638/working/building/REAL300000058000 /scratch/stefan/7769638/working /scratch/stefan/7769638
Protomer 0 (index: 1039)
Found valid previously generated 3D confromation in /scratch/stefan/7769638/working/3D/1039
`/scratch/stefan/7769638/working/3D/1039' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CNC2=O)C=C1)

`REAL300000058000.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000058000.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769638/working/building/REAL300000058000/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000058000 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CNC2=O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', '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, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 10, 10, 10, 10, 21, 21, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 10, 10, 21, 25, 25, 25, 25, 1, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 43
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000058000 none O=C([O-])C1=CC=C(NC(=O)NN=CC2=CC=CNC2=O)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', '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, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 18, 18, 18, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 18, 10, 1, 1, 1, 1, 31, 31] 31
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 83
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769638/working/building/REAL300000058000 /scratch/stefan/7769638/working /scratch/stefan/7769638

Finished preparing REAL300000058000
Recording results
/scratch/stefan/7769638/working /scratch/stefan/7769638
Appending to /scratch/stefan/7769638/finished/xaaaacf.*
0: /scratch/stefan/7769638/working/building/REAL300000058000/0.*
Removing working files in /scratch/stefan/7769638/working/building/REAL300000058000
/scratch/stefan/7769638
Compressing combined databse files
/scratch/stefan/7769638/finished/xaaaacf.db2.gz
/scratch/stefan/7769638/finished/xaaaacf.solv.gz


=======================================================
WARNING: STORE_PROTOMERS not executable or a directory!
All results left in place (/scratch/stefan/7769638/finished)
=======================================================

Finalizing...
removed `/scratch/stefan/7769638/working/3D/1040'
removed directory: `/scratch/stefan/7769638/working/3D'
`/scratch/stefan/7769638/working/protonate' -> `/scratch/stefan/7769638/archive'
`/scratch/stefan/7769638/working/input-smiles.ism' -> `/scratch/stefan/7769638/archive/input-smiles.ism'
rmdir: removing directory, `/scratch/stefan/7769638/working/building'
rmdir: removing directory, `/scratch/stefan/7769638/working'
ls: No match.
ls: No match.